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Merged
chrisgorgo merged 2 commits into from
Mar 4, 2013
Merged

New EPI dewarping workflow, in a similar manner to eddy_current correction #525

chrisgorgo merged 2 commits into from
Mar 4, 2013

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@oesteban
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@oesteban oesteban commented Feb 27, 2013

This new feature implements the EPI dewarping methodology from epidewarp.fsl,
as a workflow and including some enhancements allowing:

  • Use for dMRI
  • Optional registration
  • New EPI parameters support (parallel imaging, reverse encoding)

Additionally, some improvements on the FSL FUGUE's API have been included:

  • Added --saveshift argument support
  • Added --warp argument support
  • Improved the output listing methods for coherence

@oesteban
New EPI dewarping using a workflow
cdf352e 
This new feature implements the EPI dewarping methodology from epidewarp.fsl,
as a workflow and including some enhancements allowing:
  * Use for dMRI
  * Optional registration
  * New EPI parameters support (parallel imaging, reverse encoding)

Additionally, some improvements on the FSL FUGUE's API have been included:
  * Added --saveshift argument support
  * Added --warp argument support
  * Improved the output listing methods for coherence
oesteban
oesteban reviewed Feb 27, 2013
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nipype/interfaces/fsl/preprocess.py
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@oesteban oesteban Feb 27, 2013

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FUGUE's api changed to be more consistent with the features of this tool

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@chrisgorgo chrisgorgo Feb 27, 2013

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Does this break backward compatibility with FSL 4.1?

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@oesteban oesteban Feb 27, 2013

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No :)

@chrisgorgo
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chrisgorgo commented Feb 27, 2013

This looks excellent - thanks for the contribution. Could you please add an information to the changelog as well? Thanks!

@oesteban
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oesteban commented Feb 27, 2013

(yes), but you mean the root/CHANGES file?

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chrisgorgo commented Feb 27, 2013

yes - thanks!

@oesteban
New EPI dewarp workflow (#525)
a9a8f19 
  * Removed useless comment
  * Changelog updated
chrisgorgo added a commit that referenced this pull request Mar 4, 2013
@chrisgorgo
Merge pull request #525 from oesteban/master
68d71d8 
New EPI dewarping workflow, in a similar manner to eddy_current correction
@chrisgorgo chrisgorgo merged commit 68d71d8 into nipy:master Mar 4, 2013
@oesteban oesteban mentioned this pull request Mar 6, 2013
Merged
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into afni/resample
2a58098 
* master: (42 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into afni/to3d
784ab78 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into afni_interfaces
2d2809d 
* master:
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into connect_func
b812aea 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into enh/dcmstack
88fd4a2 
* master: (32 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into enh/vbm
1ccd02d 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into fsl_model
0328b0c 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into nipy/trim
a54558f 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into nipype_additions
3c8119f 
* master:
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into nitime
44b6585 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into spm_interfaces
9e5feaa 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into ICC
30b6b0a 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Apr 5, 2013
Merge branch 'master' into nipy/slice_motion
c60c4b9 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Apr 17, 2013
Merge branch 'master' into lif_fmri
a5fdf1c 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Apr 17, 2013
Merge branch 'master' into spm/gzip
a13768c 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Sep 11, 2013
Merge branch 'master' into mri_convert
baac8cb 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
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2 participants

@oesteban @chrisgorgo