MatlabInterface fails when script is too long

[reckbo]

Hi,

The MatlabInterface fails to run when I use a script that contains long input filenames. It looksl ike Nipype is trying to make a directory based on the script contents and the OS complains that the directory name is too long. Here's the error I get:

File "/projects/schiz/software/LabPython/lib/python2.6/site-packages/nipype-0.4.1-py2.6.egg/nipype/pipeline/plugins/multiproc.py", line 15, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/projects/schiz/software/LabPython/lib/python2.6/site-packages/nipype-0.4.1-py2.6.egg/nipype/pipeline/engine.py", line 1136, in run
outdir = make_output_dir(outdir)
File "/projects/schiz/software/LabPython/lib/python2.6/site-packages/nipype-0.4.1-py2.6.egg/nipype/pipeline/utils.py", line 455, in make_output_dir
os.makedirs(outdir)
File "/projects/schiz/software/LabPython/lib/python2.6/os.py", line 150, in makedirs
makedirs(head, mode)
File "/projects/schiz/software/LabPython/lib/python2.6/os.py", line 157, in makedirs
mkdir(name, mode)
OSError: [Errno 36] File name too long: '/tmp/tmpH_uGFp/whole_brain_nipype_workflow/_script_outfile=run_wbSC_01...net..lmi-terastation-b..mnt..array1..share..pnl..Collaborators..Inga-Germany..SC_01_DTI..SC_01-dwi-filt-ed.nhdr...net..lmi-terastation-b..mnt..array1..share..pnl..Collaborators..Inga-Germany..SC_01_DTI..Tensor_mask-SC_01-dwi-filt-Ed_AvGradient-edited.nhdr.10...tmpcopyfileoutfile..'

[satra]

sounds like it might be running into a shell limitation? is there anyway you can save the names to a local file and read it in? or could you put your script on gist.github.com

[satra]

this can now use parameterized options in config to reduce nesting depth.

https://github.com/nipy/nipype/blob/master/nipype/utils/config.py#L57