autorecon2_vol error

[alexrockhill]

I am getting an error that I have copied the stack trace below. Approximately 90% of the routine runs fine but I am not sure what happens at the end with the recon-all.

(Also I am running as a user and not as root so the error does not make it out of the Docker container)

[Node] Running "autorecon2_vol" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg
180419-13:52:23,822 interface INFO:
	 resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg
180419-13:52:26,954 workflow WARNING:
	 [Node] Error on "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" (/work/fmriprep_wf/single_subject_pp004_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol)
180419-13:52:28,556 workflow ERROR:
	 Node autorecon2_vol failed to run on host 529b8ded07df.
Traceback (most recent call last):
  File "/usr/local/miniconda/bin/fmriprep", line 11, in <module>
    load_entry_point('fmriprep==1.0.6.post2', 'console_scripts', 'fmriprep')()
  File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 267, in main
    fmriprep_wf.run(**plugin_settings)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 168, in run
    self._clean_queue(jobid, graph, result=result))
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 228, in _clean_queue
    crashfile = self._report_crash(self.procs[jobid], result=result)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 215, in _report_crash
    return report_crash(node, traceback=tb)
  File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/tools.py", line 41, in report_crash
    login_name = getpass.getuser()
  File "/usr/local/miniconda/lib/python3.6/getpass.py", line 170, in getuser
    return pwd.getpwuid(os.getuid())[0]
KeyError: 'getpwuid(): uid not found: 4190106'

[effigies]

This might be a little tricky to debug; it looks like the error you're seeing is occurring during error reporting, so we're not seeing the original error.

Can you look in <out_dir>/freesurfer/sub-pp004/scripts/recon-all.log and see if you can find the error?

For the getpwuid error, can you share your full Docker command? I suspect whatever you're doing to run as a non-root user inside Docker is what's causing that particular problem.

[alexrockhill]

Hi Chris, Thanks for looking into it. The recon-all.log is attached and the command was: docker run --rm -u 4190106:1047 -v /autofs/space/karima_004/users/learning_mri/data:/data:ro -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/out -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/work -v /autofs/space/karima_001/users/alex/software/license.txt:/opt/freesurfer/license.txt -w /work poldracklab/fmriprep:latest /data /out participant --participant_label sub-pp004 -t Learning -w /work --omp-nthreads 1 --nthreads 1 --output-space fsaverage fsnative T1w template ​ The error was only for this subject, other subjects all worked also. And one important difference was that this subject did the fmri task twice. In the <data>/mri​ directory, there were two text files and I removed one and am rerunning it but I'm not sure whether that effects anything. Thanks, Alex

…

On Thu, Apr 19, 2018 at 10:08 AM, Chris Markiewicz ***@***.*** > wrote: This might be a little tricky to debug; it looks like the error you're seeing is occurring during error reporting, so we're not seeing the original error. Can you look in <out_dir>/freesurfer/sub-pp004/scripts/recon-all.log and see if you can find the error? For the getpwuid error, can you share your full Docker command? I suspect whatever you're doing to run as a non-root user inside Docker is what's causing that particular problem. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1060 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2XKFTVtQFVj8uTBSlMnGEVW-KHvf8Uks5tqJpQgaJpZM4Tb2LM> .

-- Alex Rockhill University of Washington (206)-947-8715

[effigies]

The recon-all.log is attached

Email attachments do not make it to GitHub. You can post it as a Gist, or host it elsewhere.

docker run --rm -u 4190106:1047 -v /autofs/space/karima_004/users/learning_mri/data:/data:ro -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/out -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/work -v /autofs/space/karima_001/users/alex/software/license.txt:/opt/freesurfer/license.txt -w /work poldracklab/fmriprep:latest /data /out participant --participant_label sub-pp004 -t Learning -w /work --omp-nthreads 1 --nthreads 1 --output-space fsaverage fsnative T1w template

Okay, so you're declaring in -u 4190106:1047 that you want to run the script with UID 4190106 GID 1047 within Docker. These do not exist within the Docker container, and as far as I know there's no trivial and reliable way for you to create them immediately prior to the run.

It looks as though you're running it this way because you're on a shared computing environment, and I presume Docker has been restricted to reject its use as root? Are you able to use Singularity, instead? It's much better suited to HPC environments, and it will run programs as your user.

And one important difference was that this subject did the fmri task twice.

That shouldn't affect the surface reconstruction at all.

[alexrockhill]

Sorry, here is the Gist https://gist.github.com/alexrockhill/6dc65763bae15dd4506fbe4fbe388bcf.

…

On Thu, Apr 19, 2018 at 10:35 AM, Chris Markiewicz ***@***.*** > wrote: The recon-all.log is attached Email attachments do not make it to GitHub. You can post it as a Gist <https://gist.github.com>, or host it elsewhere. docker run --rm -u 4190106:1047 -v /autofs/space/karima_004/ users/learning_mri/data:/data:ro -v /autofs/space/karima_004/ users/learning_mri/data/derivatives/fmriprep:/out -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/work -v /autofs/space/karima_001/users/alex/software/license. txt:/opt/freesurfer/license.txt -w /work poldracklab/fmriprep:latest /data /out participant --participant_label sub-pp004 -t Learning -w /work --omp-nthreads 1 --nthreads 1 --output-space fsaverage fsnative T1w template Okay, so you're declaring in -u 4190106:1047 that you want to run the script with UID 4190106 GID 1047 within Docker. These do not exist within the Docker container, and as far as I know there's no trivial and reliable way for you to create them immediately prior to the run. It looks as though you're running it this way because you're on a shared computing environment, and I presume Docker has been restricted to reject its use as root? Are you able to use Singularity, instead? It's much better suited to HPC environments, and it will run programs as your user. And one important difference was that this subject did the fmri task twice. That shouldn't affect the surface reconstruction at all. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1060 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2XKHgRoa6EemYcRF8oIU-SBXMdSGGuks5tqKDKgaJpZM4Tb2LM> .

-- Alex Rockhill University of Washington (206)-947-8715

[alexrockhill]

Sorry to bother you but just checking if you got my Gist and had a chance to look into the error. Thanks, Alex

…

On Thu, Apr 19, 2018 at 10:51 AM, Alex Paul Rockhill ***@***.***> wrote: Sorry, here is the Gist https://gist.github.com/alexrockhill/ 6dc65763bae15dd4506fbe4fbe388bcf. On Thu, Apr 19, 2018 at 10:35 AM, Chris Markiewicz < ***@***.***> wrote: > The recon-all.log is attached > > Email attachments do not make it to GitHub. You can post it as a Gist > <https://gist.github.com>, or host it elsewhere. > > docker run --rm -u 4190106:1047 -v /autofs/space/karima_004/users/learning_mri/data:/data:ro > -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/out > -v /autofs/space/karima_004/users/learning_mri/data/derivatives/fmriprep:/work > -v /autofs/space/karima_001/users/alex/software/license.txt:/opt/freesurfer/license.txt > -w /work poldracklab/fmriprep:latest /data /out participant > --participant_label sub-pp004 -t Learning -w /work --omp-nthreads 1 > --nthreads 1 --output-space fsaverage fsnative T1w template > > Okay, so you're declaring in -u 4190106:1047 that you want to run the > script with UID 4190106 GID 1047 within Docker. These do not exist within > the Docker container, and as far as I know there's no trivial and reliable > way for you to create them immediately prior to the run. > > It looks as though you're running it this way because you're on a shared > computing environment, and I presume Docker has been restricted to reject > its use as root? Are you able to use Singularity, instead? It's much better > suited to HPC environments, and it will run programs as your user. > > And one important difference was that this subject did the fmri task > twice. > > That shouldn't affect the surface reconstruction at all. > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#1060 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AM2XKHgRoa6EemYcRF8oIU-SBXMdSGGuks5tqKDKgaJpZM4Tb2LM> > . > -- Alex Rockhill University of Washington (206)-947-8715

-- Alex Rockhill University of Washington (206)-947-8715

[effigies]

Ah sorry for not responding. No, there are no errors in that gist. Without that, and given that it was unable to write the error log, I don't think we can debug it from this information.

Perhaps we can address the reasons that you're running Docker with -u 4190106:1047. With some more information about your environment and requirements, perhaps we can come up with a better solution.

Quoted from #1060 (comment) for context:

Okay, so you're declaring in -u 4190106:1047 that you want to run the script with UID 4190106 GID 1047 within Docker. These do not exist within the Docker container, and as far as I know there's no trivial and reliable way for you to create them immediately prior to the run.

It looks as though you're running it this way because you're on a shared computing environment, and I presume Docker has been restricted to reject its use as root? Are you able to use Singularity, instead? It's much better suited to HPC environments, and it will run programs as your user.

[alexrockhill]

Hey Chris, I am running it now as root and I will send you the same log file if it errors out. The reason I ran it as a user is because I don't have root privileges and so any folders or files created will not be able to be deleted by me. I will let you know in ~6 hours if there was an error and the error log. Thanks, Alex

…

On Mon, Apr 23, 2018 at 1:55 PM, Chris Markiewicz ***@***.***> wrote: Ah sorry for not responding. No, there are no errors in that gist. Without that, and given that it was unable to write the error log, I don't think we can debug it from this information. Perhaps we can address the reasons that you're running Docker with -u 4190106:1047. With some more information about your environment and requirements, perhaps we can come up with a better solution. Quoted from #1060 (comment) <#1060 (comment)> for context: Okay, so you're declaring in -u 4190106:1047 that you want to run the script with UID 4190106 GID 1047 within Docker. These do not exist within the Docker container, and as far as I know there's no trivial and reliable way for you to create them immediately prior to the run. It looks as though you're running it this way because you're on a shared computing environment, and I presume Docker has been restricted to reject its use as root? Are you able to use Singularity, instead? It's much better suited to HPC environments, and it will run programs as your user. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#1060 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AM2XKBqDUgxZhRwBYORdXHUvGZ8jEJhlks5trhWpgaJpZM4Tb2LM> .

-- Alex Rockhill University of Washington (206)-947-8715

[alexrockhill]

Hi Chris, Here are the contents of the recon-all.log run as root. Tue Apr 10 15:50:19 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-pp004/anat/sub-pp004_T1w.nii -noskullstrip -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11711204 13923652 245728 40054848 52962560 Swap: 65535996 1562004 63973992 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-pp004 mri_convert /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz mri_convert.bin /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-pp004/anat/sub-pp004_T1w.nii... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) writing to /out/freesurfer/sub-pp004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 10 15:50:27 UTC 2018 Found 1 runs /out/freesurfer/sub-pp004/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-pp004/mri/orig/001.mgz /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004 mri_convert /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-pp004/mri/rawavg.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-pp004/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm /out/freesurfer/sub-pp004/mri/orig.mgz /out/freesurfer/sub-pp004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Apr 10 15:50:35 UTC 2018 /out/freesurfer/sub-pp004/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:50:35 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4850 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4850/nu0.mnc...

…

-------------------------------------------------------- Iteration 1 Tue Apr 10 15:50:37 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ -iterations 1000 -distance 50 [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:50:37] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 44 CV of field change: 0.000991484 mri_convert ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4850/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue Apr 10 15:51:34 UTC 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Apr 10 15:51:34 UTC 2018 Ended at Tue Apr 10 15:52:03 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 10 15:52:05 UTC 2018 /out/freesurfer/sub-pp004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8076, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log TalAviQA: 0.97630 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Apr 10 15:52:05 UTC 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:52:05 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.5617 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5617/nu0.mnc...

-------------------------------------------------------- Iteration 1 Tue Apr 10 15:52:07 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:07] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.000958689

-------------------------------------------------------- Iteration 2 Tue Apr 10 15:52:47 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:47] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.000966384 mri_binarize --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-pp004/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN input ./tmp.mri_nu_correct.mni.5617/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5617/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading ./tmp.mri_nu_correct.mni.5617/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5617/nu2.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc mul .99652211832853307612 Saving result to './tmp.mri_nu_correct.mni.5617/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.5617/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (31, 141) to ( 3, 110) Tue Apr 10 15:54:01 UTC 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Apr 10 15:54:01 UTC 2018 /out/freesurfer/sub-pp004/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.09857 -0.00706 -0.00922 0.64290; -0.00426 1.02814 0.23780 -41.54960; 0.00447 -0.17302 1.10501 -11.64378; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 49 seconds. Started at Tue Apr 10 15:50:19 UTC 2018 Ended at Tue Apr 10 15:55:51 UTC 2018 #@#%# recon-all-run-time-hours 0.092 recon-all -s sub-pp004 finished without error at Tue Apr 10 15:55:51 UTC 2018 New invocation of recon-all Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11729200 13659560 245728 40300944 52944112 Swap: 65535996 1561372 63974624 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004/mri mri_em_register -rusage /out/freesurfer/sub-pp004/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 38, 41) --> (191, 154, 198) using (106, 77, 120) as brain centroid... mean wm in atlas = 107, using box (90,63,101) --> (121, 91,139) to find MRI wm before smoothing, mri peak at 98 robust fit to distribution - 98 +- 5.3 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.511 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.053168 @ (-9.091, 27.273, -9.091) max log p = -3.979448 @ (4.545, -4.545, 4.545) max log p = -3.932829 @ (2.273, -2.273, -2.273) max log p = -3.914850 @ (-1.136, -1.136, -1.136) max log p = -3.912519 @ (2.841, 6.250, 2.841) max log p = -3.905882 @ (1.420, 1.420, -0.284) Found translation: (0.9, 27.0, -5.4): log p = -3.906 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.797, old_max_log_p =-3.906 (thresh=-3.9) 1.06375 0.00000 0.00000 -7.17288; 0.00000 1.22023 0.18169 -13.47781; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.796, old_max_log_p =-3.797 (thresh=-3.8) 1.05465 0.15927 0.02372 -23.35695; -0.12843 1.11905 0.16663 13.69829; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.600, old_max_log_p =-3.796 (thresh=-3.8) 1.08129 0.05090 -0.00067 -15.80799; -0.02583 1.18861 0.21567 -10.94858; 0.00859 -0.15189 1.04557 2.48901; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.600 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.594 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.573, old_max_log_p =-3.594 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03459 1.16179 0.22867 -9.72511; -0.00032 -0.17423 1.06153 3.95661; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.572, old_max_log_p =-3.573 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.572 (old=-4.511) transform before final EM align: 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 011: -log(p) = 4.0 tol 0.000000 final transform: 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... mri_em_register utimesec 643.413249 mri_em_register stimesec 3.760615 mri_em_register ru_maxrss 599108 mri_em_register ru_ixrss 0 mri_em_register ru_idrss 0 mri_em_register ru_isrss 0 mri_em_register ru_minflt 1134670 mri_em_register ru_majflt 7 mri_em_register ru_nswap 0 mri_em_register ru_inblock 142160 mri_em_register ru_oublock 16 mri_em_register ru_msgsnd 0 mri_em_register ru_msgrcv 0 mri_em_register ru_nsignals 0 mri_em_register ru_nvcsw 10 mri_em_register ru_nivcsw 751 registration took 10 minutes and 47 seconds. #-------------------------------------- #@# CA Normalize Tue Apr 10 16:07:52 UTC 2018 /out/freesurfer/sub-pp004/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 38, 41) --> (191, 154, 198) using (106, 77, 120) as brain centroid... mean wm in atlas = 107, using box (90,63,101) --> (121, 91,139) to find MRI wm before smoothing, mri peak at 98 robust fit to distribution - 98 +- 5.3 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 using 246344 sample points... INFO: compute sample coordinates transform 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 36, 39) --> (189, 135, 193) Left_Cerebral_White_Matter: limiting intensities to 96.0 --> 132.0 0 of 4240 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (67, 37, 38) --> (130, 133, 194)

[alexrockhill]

Hey Chris, Sorry to bother you, did you get a chance to look at the log file to see if there was an easy fix? Thanks, Alex

…

On Tue, Apr 24, 2018 at 5:31 PM, Alex Paul Rockhill ***@***.***> wrote: Hi Chris, Here are the contents of the recon-all.log run as root. Tue Apr 10 15:50:19 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-pp004/anat/sub-pp004_T1w.nii -noskullstrip -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11711204 13923652 245728 40054848 52962560 Swap: 65535996 1562004 63973992 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-pp004 mri_convert /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz mri_convert.bin /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-pp004/anat/sub-pp004_T1w.nii... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) writing to /out/freesurfer/sub-pp004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 10 15:50:27 UTC 2018 Found 1 runs /out/freesurfer/sub-pp004/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-pp004/mri/orig/001.mgz /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004 mri_convert /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-pp004/mri/rawavg.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-pp004/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm /out/freesurfer/sub-pp004/mri/orig.mgz /out/freesurfer/sub-pp004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Apr 10 15:50:35 UTC 2018 /out/freesurfer/sub-pp004/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:50:35 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4850 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4850/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Apr 10 15:50:37 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ -iterations 1000 -distance 50 ***@***.***:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:50:37] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.imp Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Number of iterations: 44 CV of field change: 0.000991484 mri_convert ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4850/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue Apr 10 15:51:34 UTC 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Apr 10 15:51:34 UTC 2018 Ended at Tue Apr 10 15:52:03 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 10 15:52:05 UTC 2018 /out/freesurfer/sub-pp004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8076, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log TalAviQA: 0.97630 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Apr 10 15:52:05 UTC 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:52:05 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.5617 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5617/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Apr 10 15:52:07 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ***@***.***:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:07] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.imp Processing:................................................. ................Done 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Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Number of iterations: 41 CV of field change: 0.000958689 -------------------------------------------------------- Iteration 2 Tue Apr 10 15:52:47 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ***@***.***:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:47] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.imp Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. 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./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-pp004/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN input ./tmp.mri_nu_correct.mni.5617/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5617/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading ./tmp.mri_nu_correct.mni.5617/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5617/nu2.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc mul .99652211832853307612 Saving result to './tmp.mri_nu_correct.mni.5617/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.5617/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (31, 141) to ( 3, 110) Tue Apr 10 15:54:01 UTC 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Apr 10 15:54:01 UTC 2018 /out/freesurfer/sub-pp004/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.09857 -0.00706 -0.00922 0.64290; -0.00426 1.02814 0.23780 -41.54960; 0.00447 -0.17302 1.10501 -11.64378; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 49 seconds. Started at Tue Apr 10 15:50:19 UTC 2018 Ended at Tue Apr 10 15:55:51 UTC 2018 #@#%# recon-all-run-time-hours 0.092 recon-all -s sub-pp004 finished without error at Tue Apr 10 15:55:51 UTC 2018 New invocation of recon-all Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11729200 13659560 245728 40300944 52944112 Swap: 65535996 1561372 63974624 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004/mri mri_em_register -rusage /out/freesurfer/sub-pp004/ touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 38, 41) --> (191, 154, 198) using (106, 77, 120) as brain centroid... mean wm in atlas = 107, using box (90,63,101) --> (121, 91,139) to find MRI wm before smoothing, mri peak at 98 robust fit to distribution - 98 +- 5.3 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.511 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.053168 @ (-9.091, 27.273, -9.091) max log p = -3.979448 @ (4.545, -4.545, 4.545) max log p = -3.932829 @ (2.273, -2.273, -2.273) max log p = -3.914850 @ (-1.136, -1.136, -1.136) max log p = -3.912519 @ (2.841, 6.250, 2.841) max log p = -3.905882 @ (1.420, 1.420, -0.284) Found translation: (0.9, 27.0, -5.4): log p = -3.906 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.797, old_max_log_p =-3.906 (thresh=-3.9) 1.06375 0.00000 0.00000 -7.17288; 0.00000 1.22023 0.18169 -13.47781; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.796, old_max_log_p =-3.797 (thresh=-3.8) 1.05465 0.15927 0.02372 -23.35695; -0.12843 1.11905 0.16663 13.69829; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.600, old_max_log_p =-3.796 (thresh=-3.8) 1.08129 0.05090 -0.00067 -15.80799; -0.02583 1.18861 0.21567 -10.94858; 0.00859 -0.15189 1.04557 2.48901; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.600 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.594 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.573, old_max_log_p =-3.594 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03459 1.16179 0.22867 -9.72511; -0.00032 -0.17423 1.06153 3.95661; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.572, old_max_log_p =-3.573 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; outof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.572 (old=-4.511) transform before final EM align: 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0

[effigies]

Sorry. Looking at it, there's no error reported. Were you able to get a crash dump from running as root?

[alexrockhill]

Hey Chris, Here is the command line error: [Node] Setting-up "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/work/fmriprep_wf/single_subject_pp004_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". 180427-15:10:41,558 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-15:10:41,559 workflow INFO: [Node] Running "autorecon2_vol" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-15:10:41,561 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-15:10:47,471 workflow WARNING: [Node] Error on "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" (/work/fmriprep_wf/single_subject_pp004_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol) 180427-15:10:48,999 workflow ERROR: Node autorecon2_vol failed to run on host 0318f5b20fd4. 180427-15:10:49,141 workflow ERROR: Saving crash info to /out/fmriprep/sub-pp004/log/20180427-124219_89adb719-79c2-47b9-941a-47ec92bff3ab/crash-20180427-151049-root-autorecon2_vol-77a749b2-af7a-4371-b705-d6246b95f491.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 487, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 1023, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 960, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer -rw-rw-r-- 1 4190106 1047 241643 Apr 24 19:08 /out/freesurfer/sub-pp004/scripts/recon-all.log Linux 0318f5b20fd4 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ERROR: it appears that recon-all is already running for sub-pp004 based on the presence of /out/freesurfer/sub-pp004/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /out/freesurfer/sub-pp004/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: ---------------------------------------------------------- ------------------------------ SUBJECT sub-pp004 HEMI lh rh DATE Tue Apr 10 15:57:04 UTC 2018 USER unknown HOST 89c04352d906 PROCESSID 6798 PROCESSOR x86_64 OS Linux Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ ---------------------------------------------------------- Standard error: Return code: 1 180427-15:10:50,998 workflow ERROR: could not run node: fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol 180427-15:10:51,295 cli WARNING: Errors occurred while generating reports for participants: pp004 (1).

…

--------------------------------------------------------------------------------------------------------------------------------------------------- And here is the most up to date log file: Tue Apr 10 15:50:19 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-pp004/anat/sub-pp004_T1w.nii -noskullstrip -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11711204 13923652 245728 40054848 52962560 Swap: 65535996 1562004 63973992 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-pp004 mri_convert /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz mri_convert.bin /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-pp004/anat/sub-pp004_T1w.nii... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) writing to /out/freesurfer/sub-pp004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 10 15:50:27 UTC 2018 Found 1 runs /out/freesurfer/sub-pp004/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-pp004/mri/orig/001.mgz /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004 mri_convert /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-pp004/mri/rawavg.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-pp004/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm /out/freesurfer/sub-pp004/mri/orig.mgz /out/freesurfer/sub-pp004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Apr 10 15:50:35 UTC 2018 /out/freesurfer/sub-pp004/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:50:35 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4850 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4850/nu0.mnc...

-------------------------------------------------------- Iteration 1 Tue Apr 10 15:50:37 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ -iterations 1000 -distance 50 [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:50:37] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 44 CV of field change: 0.000991484 mri_convert ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4850/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue Apr 10 15:51:34 UTC 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Apr 10 15:51:34 UTC 2018 Ended at Tue Apr 10 15:52:03 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 10 15:52:05 UTC 2018 /out/freesurfer/sub-pp004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8076, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log TalAviQA: 0.97630 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Apr 10 15:52:05 UTC 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:52:05 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.5617 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5617/nu0.mnc...

-------------------------------------------------------- Iteration 1 Tue Apr 10 15:52:07 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:07] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.000958689

-------------------------------------------------------- Iteration 2 Tue Apr 10 15:52:47 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:47] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.000966384 mri_binarize --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-pp004/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN input ./tmp.mri_nu_correct.mni.5617/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5617/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading ./tmp.mri_nu_correct.mni.5617/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5617/nu2.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc mul .99652211832853307612 Saving result to './tmp.mri_nu_correct.mni.5617/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.5617/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (31, 141) to ( 3, 110) Tue Apr 10 15:54:01 UTC 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Apr 10 15:54:01 UTC 2018 /out/freesurfer/sub-pp004/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.09857 -0.00706 -0.00922 0.64290; -0.00426 1.02814 0.23780 -41.54960; 0.00447 -0.17302 1.10501 -11.64378; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 49 seconds. Started at Tue Apr 10 15:50:19 UTC 2018 Ended at Tue Apr 10 15:55:51 UTC 2018 #@#%# recon-all-run-time-hours 0.092 recon-all -s sub-pp004 finished without error at Tue Apr 10 15:55:51 UTC 2018 New invocation of recon-all Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11729200 13659560 245728 40300944 52944112 Swap: 65535996 1561372 63974624 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004/mri mri_em_register -rusage /out/freesurfer/sub-pp004/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 38, 41) --> (191, 154, 198) using (106, 77, 120) as brain centroid... mean wm in atlas = 107, using box (90,63,101) --> (121, 91,139) to find MRI wm before smoothing, mri peak at 98 robust fit to distribution - 98 +- 5.3 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.511 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.053168 @ (-9.091, 27.273, -9.091) max log p = -3.979448 @ (4.545, -4.545, 4.545) max log p = -3.932829 @ (2.273, -2.273, -2.273) max log p = -3.914850 @ (-1.136, -1.136, -1.136) max log p = -3.912519 @ (2.841, 6.250, 2.841) max log p = -3.905882 @ (1.420, 1.420, -0.284) Found translation: (0.9, 27.0, -5.4): log p = -3.906 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.797, old_max_log_p =-3.906 (thresh=-3.9) 1.06375 0.00000 0.00000 -7.17288; 0.00000 1.22023 0.18169 -13.47781; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.796, old_max_log_p =-3.797 (thresh=-3.8) 1.05465 0.15927 0.02372 -23.35695; -0.12843 1.11905 0.16663 13.69829; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.600, old_max_log_p =-3.796 (thresh=-3.8) 1.08129 0.05090 -0.00067 -15.80799; -0.02583 1.18861 0.21567 -10.94858; 0.00859 -0.15189 1.04557 2.48901; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.600 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.594 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.573, old_max_log_p =-3.594 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03459 1.16179 0.22867 -9.72511; -0.00032 -0.17423 1.06153 3.95661; 0.00000

[alexrockhill]

Any idea what's going on? It looks like it says failed to run on host.

…

On Fri, Apr 27, 2018 at 12:23 PM, Alex Paul Rockhill ***@***.***> wrote: Hey Chris, Here is the command line error: [Node] Setting-up "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf. surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/work/fmriprep_wf/single_subject_pp004_wf/anat_preproc_ wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". 180427-15:10:41,558 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-15:10:41,559 workflow INFO: [Node] Running "autorecon2_vol" ("niworkflows.nipype. interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-15:10:41,561 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-15:10:47,471 workflow WARNING: [Node] Error on "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf. surface_recon_wf.autorecon_resume_wf.autorecon2_vol" (/work/fmriprep_wf/single_subject_pp004_wf/anat_preproc_ wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol) 180427-15:10:48,999 workflow ERROR: Node autorecon2_vol failed to run on host 0318f5b20fd4. 180427-15:10:49,141 workflow ERROR: Saving crash info to /out/fmriprep/sub-pp004/log/ 20180427-124219_89adb719-79c2-47b9-941a-47ec92bff3ab/crash- 20180427-151049-root-autorecon2_vol-77a749b2-af7a- 4371-b705-d6246b95f491.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/pipeline/plugins/multiproc.py", line 68, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/pipeline/engine/nodes.py", line 487, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/interfaces/base/core.py", line 516, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/interfaces/base/core.py", line 1023, in _run_interface self.raise_exception(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/ niworkflows/nipype/interfaces/base/core.py", line 960, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg Standard output: Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a INFO: SUBJECTS_DIR is /out/freesurfer Actual FREESURFER_HOME /opt/freesurfer -rw-rw-r-- 1 4190106 1047 241643 Apr 24 19:08 /out/freesurfer/sub-pp004/ scripts/recon-all.log Linux 0318f5b20fd4 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux ERROR: it appears that recon-all is already running for sub-pp004 based on the presence of /out/freesurfer/sub-pp004/scripts/IsRunning.lh+rh. It could also be that recon-all was running at one point but died in an unexpected way. If it is the case that there is a process running, you can kill it and start over or just let it run. If the process has died, you should type: rm /out/freesurfer/sub-pp004/scripts/IsRunning.lh+rh and re-run. Or you can add -no-isrunning to the recon-all command-line. The contents of this file are: ---------------------------------------------------------- ------------------------------ SUBJECT sub-pp004 HEMI lh rh DATE Tue Apr 10 15:57:04 UTC 2018 USER unknown HOST 89c04352d906 PROCESSID 6798 PROCESSOR x86_64 OS Linux Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ ---------------------------------------------------------- Standard error: Return code: 1 180427-15:10:50,998 workflow ERROR: could not run node: fmriprep_wf.single_subject_ pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_ resume_wf.autorecon2_vol 180427-15:10:51,295 cli WARNING: Errors occurred while generating reports for participants: pp004 (1). ------------------------------------------------------------ ------------------------------------------------------------ --------------------------- And here is the most up to date log file: Tue Apr 10 15:50:19 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-pp004/anat/sub-pp004_T1w.nii -noskullstrip -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11711204 13923652 245728 40054848 52962560 Swap: 65535996 1562004 63973992 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-pp004 mri_convert /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz mri_convert.bin /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-pp004/anat/sub-pp004_T1w.nii... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) writing to /out/freesurfer/sub-pp004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 10 15:50:27 UTC 2018 Found 1 runs /out/freesurfer/sub-pp004/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-pp004/mri/orig/001.mgz /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004 mri_convert /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-pp004/mri/rawavg.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-pp004/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm /out/freesurfer/sub-pp004/mri/orig.mgz /out/freesurfer/sub-pp004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Apr 10 15:50:35 UTC 2018 /out/freesurfer/sub-pp004/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:50:35 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4850 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4850/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Apr 10 15:50:37 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ -iterations 1000 -distance 50 ***@***.***:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:50:37] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.imp Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Number of iterations: 44 CV of field change: 0.000991484 mri_convert ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4850/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue Apr 10 15:51:34 UTC 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Apr 10 15:51:34 UTC 2018 Ended at Tue Apr 10 15:52:03 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 10 15:52:05 UTC 2018 /out/freesurfer/sub-pp004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8076, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log TalAviQA: 0.97630 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Apr 10 15:52:05 UTC 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:52:05 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.5617 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5617/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Apr 10 15:52:07 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ***@***.***:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:07] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.imp Processing:................................................. ................Done 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Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Number of iterations: 41 CV of field change: 0.000958689 -------------------------------------------------------- Iteration 2 Tue Apr 10 15:52:47 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ***@***.***:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:47] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.imp Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. ................Done Processing:................................................. 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./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-pp004/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN input ./tmp.mri_nu_correct.mni.5617/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5617/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading ./tmp.mri_nu_correct.mni.5617/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5617/nu2.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc mul .99652211832853307612 Saving result to './tmp.mri_nu_correct.mni.5617/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.5617/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (31, 141) to ( 3, 110) Tue Apr 10 15:54:01 UTC 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Apr 10 15:54:01 UTC 2018 /out/freesurfer/sub-pp004/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.09857 -0.00706 -0.00922 0.64290; -0.00426 1.02814 0.23780 -41.54960; 0.00447 -0.17302 1.10501 -11.64378; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 49 seconds. Started at Tue Apr 10 15:50:19 UTC 2018 Ended at Tue Apr 10 15:55:51 UTC 2018 #@#%# recon-all-run-time-hours 0.092 recon-all -s sub-pp004 finished without error at Tue Apr 10 15:55:51 UTC 2018 New invocation of recon-all Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11729200 13659560 245728 40300944 52944112 Swap: 65535996 1561372 63974624 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by ***@***.*** (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004/mri mri_em_register -rusage /out/freesurfer/sub-pp004/ touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 38, 41) --> (191, 154, 198) using (106, 77, 120) as brain centroid... mean wm in atlas = 107, using box (90,63,101) --> (121, 91,139) to find MRI wm before smoothing, mri peak at 98 robust fit to distribution - 98 +- 5.3 af

[effigies]

Ah. Yeah, sorry, this is an annoying thing about working with FreeSurfer. There are scripts/IsRunning* files that it creates while running, to keep other copies of itself from running. When it crashes, those don't get removed, and they need to be removed manually to resume.

You should remove <out_dir>/freesurfer/sub-*/scripts/IsRunning*, and try again.

This may or may not be the source of the original error.

[alexrockhill]

Hey Chris, So I think the previous error was just due to running the process multiple times due to the original error reproduced below. The log file is also copied below, but curiously it looks as if recon-all finished without error on the last go round. Any help again would be appreciated. Thanks, Alex [Node] Running "autorecon2_vol" ("niworkflows.nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command: recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-20:40:22,56 interface INFO: resume recon-all : recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer -nogcareg -nocanorm -nocareg 180427-21:30:17,966 workflow INFO: [Node] Finished "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol". 180427-21:30:19,104 workflow WARNING: [Node] Error on "fmriprep_wf.single_subject_pp004_wf.ds_summary_report" (/work/fmriprep_wf/single_subject_pp004_wf/ds_summary_report) 180427-21:30:19,106 workflow ERROR: Node ds_summary_report failed to run on host e74cf83be0aa. Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 339, in _send_procs_to_workers self.procs[jobid].run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 487, in run result = self._run_interface(execute=True) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 571, in _run_interface return self._run_command(execute) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 650, in _run_command result = self._interface.run(cwd=outdir) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/interfaces/base/core.py", line 516, in run runtime = self._run_interface(runtime) File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/interfaces/bids.py", line 253, in _run_interface copy(fname, out_file) File "/usr/local/miniconda/lib/python3.6/shutil.py", line 235, in copy copyfile(src, dst, follow_symlinks=follow_symlinks) File "/usr/local/miniconda/lib/python3.6/shutil.py", line 115, in copyfile with open(dst, 'wb') as fdst: PermissionError: [Errno 13] Permission denied: '/work/reportlets/fmriprep/sub-pp004/anat/sub-pp004_T1w_summary.html' During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/miniconda/bin/fmriprep", line 11, in <module> load_entry_point('fmriprep==1.0.6.post2', 'console_scripts', 'fmriprep')() File "/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py", line 267, in main fmriprep_wf.run(**plugin_settings) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run runner.run(execgraph, updatehash=updatehash, config=self.config) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 190, in run self._send_procs_to_workers(updatehash=updatehash, graph=graph) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 347, in _send_procs_to_workers 'traceback': traceback File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 228, in _clean_queue crashfile = self._report_crash(self.procs[jobid], result=result) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 215, in _report_crash return report_crash(node, traceback=tb) File "/usr/local/miniconda/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/tools.py", line 41, in report_crash login_name = getpass.getuser() File "/usr/local/miniconda/lib/python3.6/getpass.py", line 170, in getuser return pwd.getpwuid(os.getuid())[0] KeyError: 'getpwuid(): uid not found: 4190106' Tue Apr 10 15:50:19 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon1 -i /data/sub-pp004/anat/sub-pp004_T1w.nii -noskullstrip -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11711204 13923652 245728 40054848 52962560 Swap: 65535996 1562004 63973992 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:19-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:50:20-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /out/freesurfer/sub-pp004 mri_convert /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz mri_convert.bin /data/sub-pp004/anat/sub-pp004_T1w.nii /out/freesurfer/sub-pp004/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/sub-pp004/anat/sub-pp004_T1w.nii... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) writing to /out/freesurfer/sub-pp004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Tue Apr 10 15:50:27 UTC 2018 Found 1 runs /out/freesurfer/sub-pp004/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /out/freesurfer/sub-pp004/mri/orig/001.mgz /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004 mri_convert /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform mri_convert.bin /out/freesurfer/sub-pp004/mri/rawavg.mgz /out/freesurfer/sub-pp004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /out/freesurfer/sub-pp004/mri/rawavg.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99888, -0.00778031, 0.0466629) j_ras = (0.00704131, 0.999848, 0.0159806) k_ras = (-0.0467801, -0.0156341, 0.998783) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /out/freesurfer/sub-pp004/mri/orig.mgz... mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm /out/freesurfer/sub-pp004/mri/orig.mgz /out/freesurfer/sub-pp004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Apr 10 15:50:35 UTC 2018 /out/freesurfer/sub-pp004/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:50:35 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.4850 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.4850/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4850/nu0.mnc...

…

-------------------------------------------------------- Iteration 1 Tue Apr 10 15:50:37 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ -iterations 1000 -distance 50 [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:50:37] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4850/0/ ./tmp.mri_nu_correct.mni.4850/nu0.mnc ./tmp.mri_nu_correct.mni.4850/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 44 CV of field change: 0.000991484 mri_convert ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.4850/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4850/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Tue Apr 10 15:51:34 UTC 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Tue Apr 10 15:51:34 UTC 2018 Ended at Tue Apr 10 15:52:03 UTC 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Apr 10 15:52:05 UTC 2018 /out/freesurfer/sub-pp004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.8076, pval=0.8469 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log tal_QC_AZS /out/freesurfer/sub-pp004/mri/transforms/talairach_avi.log TalAviQA: 0.97630 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Apr 10 15:52:05 UTC 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /out/freesurfer/sub-pp004/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 10 15:52:05 UTC 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.5617 /out/freesurfer/sub-pp004/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.5617/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=2510.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5617/nu0.mnc...

-------------------------------------------------------- Iteration 1 Tue Apr 10 15:52:07 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:07] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/0/ ./tmp.mri_nu_correct.mni.5617/nu0.mnc ./tmp.mri_nu_correct.mni.5617/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 41 CV of field change: 0.000958689

-------------------------------------------------------- Iteration 2 Tue Apr 10 15:52:47 UTC 2018 nu_correct -clobber ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ [@89c04352d906:/out/freesurfer/sub-pp004/mri/] [2018-04-10 15:52:47] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.5617/1/ ./tmp.mri_nu_correct.mni.5617/nu1.mnc ./tmp.mri_nu_correct.mni.5617/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 35 CV of field change: 0.000966384 mri_binarize --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /out/freesurfer/sub-pp004/mri cmdline mri_binarize.bin --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5617/ones.mgz sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN input ./tmp.mri_nu_correct.mni.5617/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5617/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777216 voxels in final mask Count: 16777216 16777216.000000 16777216 100.000000 mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/input.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5617/ones.mgz --i ./tmp.mri_nu_correct.mni.5617/nu2.mnc --sum ./tmp.mri_nu_correct.mni.5617/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5617/output.mean.dat sysname Linux hostname 89c04352d906 machine x86_64 user UNKNOWN UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5617/ones.mgz Loading ./tmp.mri_nu_correct.mni.5617/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.5617/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5617/nu2.mnc ./tmp.mri_nu_correct.mni.5617/nu2.mnc mul .99652211832853307612 Saving result to './tmp.mri_nu_correct.mni.5617/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz mri_convert.bin ./tmp.mri_nu_correct.mni.5617/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.5617/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.16415e-10, 3.72529e-09) j_ras = (3.72529e-09, 9.31323e-10, -1) k_ras = (1.74623e-10, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping (31, 141) to ( 3, 110) Tue Apr 10 15:54:01 UTC 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /out/freesurfer/sub-pp004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Apr 10 15:54:01 UTC 2018 /out/freesurfer/sub-pp004/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.09857 -0.00706 -0.00922 0.64290; -0.00426 1.02814 0.23780 -41.54960; 0.00447 -0.17302 1.10501 -11.64378; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 18 Starting OpenSpline(): npoints = 18 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 51 (51), valley at 23 (23) csf peak at 26, setting threshold to 42 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 49 seconds. Started at Tue Apr 10 15:50:19 UTC 2018 Ended at Tue Apr 10 15:55:51 UTC 2018 #@#%# recon-all-run-time-hours 0.092 recon-all -s sub-pp004 finished without error at Tue Apr 10 15:55:51 UTC 2018 New invocation of recon-all Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004 /opt/freesurfer/bin/recon-all -autorecon2-volonly -openmp 1 -subjid sub-pp004 -sd /out/freesurfer subjid sub-pp004 setenv SUBJECTS_DIR /out/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a Linux 89c04352d906 3.10.0-693.11.1.el7.x86_64 #1 SMP Mon Dec 4 23:52:40 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 65536 memorylocked 64 kbytes maxproc unlimited maxlocks unlimited maxsignal 256450 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65689704 11729200 13659560 245728 40300944 52944112 Swap: 65535996 1561372 63974624 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/04/10-15:57:04-GMT BuildTimeStamp: Oct 20 2017 13:59:15 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: UNKNOWN Machine: 89c04352d906 Platform: Linux PlatformVersion: 3.10.0-693.11.1.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /opt/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #------------------------------------- #@# EM Registration Tue Apr 10 15:57:04 UTC 2018 /out/freesurfer/sub-pp004/mri mri_em_register -rusage /out/freesurfer/sub-pp004/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (64, 38, 41) --> (191, 154, 198) using (106, 77, 120) as brain centroid... mean wm in atlas = 107, using box (90,63,101) --> (121, 91,139) to find MRI wm before smoothing, mri peak at 98 robust fit to distribution - 98 +- 5.3 after smoothing, mri peak at 98, scaling input intensities by 1.092 scaling channel 0 by 1.09184 initial log_p = -4.511 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.053168 @ (-9.091, 27.273, -9.091) max log p = -3.979448 @ (4.545, -4.545, 4.545) max log p = -3.932829 @ (2.273, -2.273, -2.273) max log p = -3.914850 @ (-1.136, -1.136, -1.136) max log p = -3.912519 @ (2.841, 6.250, 2.841) max log p = -3.905882 @ (1.420, 1.420, -0.284) Found translation: (0.9, 27.0, -5.4): log p = -3.906 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.797, old_max_log_p =-3.906 (thresh=-3.9) 1.06375 0.00000 0.00000 -7.17288; 0.00000 1.22023 0.18169 -13.47781; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.796, old_max_log_p =-3.797 (thresh=-3.8) 1.05465 0.15927 0.02372 -23.35695; -0.12843 1.11905 0.16663 13.69829; 0.00000 -0.11999 1.07125 -2.22048; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.600, old_max_log_p =-3.796 (thresh=-3.8) 1.08129 0.05090 -0.00067 -15.80799; -0.02583 1.18861 0.21567 -10.94858; 0.00859 -0.15189 1.04557 2.48901; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.600 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.594, old_max_log_p =-3.594 (thresh=-3.6) 1.08099 0.04591 0.03354 -19.10028; -0.02535 1.16632 0.21162 -10.38161; -0.02729 -0.15635 1.06463 5.36615; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.573, old_max_log_p =-3.594 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03459 1.16179 0.22867 -9.72511; -0.00032 -0.17423 1.06153 3.95661; 0.00000 0.00000 0.00000 1.00000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.572, old_max_log_p =-3.573 (thresh=-3.6) 1.07981 0.05964 0.00937 -18.01642; -0.03463 1.16316 0.22894 -9.87629; -0.00032 -0.17403 1.06028 4.07554; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentu

[effigies]

• [Node] Finished "fmriprep_wf.single_subject_pp004_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".

Looks good. So it could've been some kind of stochastic error, followed by forgetting to remove the IsRunning files.

• PermissionError: [Errno 13] Permission denied: '/work/reportlets/fmriprep/sub-pp004/anat/sub-pp004_T1w_summary.html'

This is a permission error. Could be that you ran things as root before, and so you no longer have write permissions for those directories. Sorry my earlier suggestion sent you down that path.

• KeyError: 'getpwuid(): uid not found: 4190106'

This is that secondary error again which prevents writing crashfiles. There's not much fix for that at the moment. We can try to get nipype to have a decent fallback in those cases, but it's a pretty unusual error. One thing you could try that might resolve it is adding -v /etc/passwd:/etc/passwd:ro to your Docker command. I don't know that that will work, but if getpwuid is just parsing /etc/passwd to match UID to username, that could be a quick fix.

I still don't see anything in your FreeSurfer output indicating what the initial issue might have been.