debug 'folder does not exist' error when running feat

[jokedurnez]

Feat was expecting lower level .feat folders, when running interfaces.fsl.model.FEATModel(). This suggestion fixes the bug.

[jokedurnez]

The reason why this test fails has nothing to do with the suggested fix.

[jokedurnez]

Btw, this is the error without fix:

170509-17:57:04,646 interface INFO:
         stderr 2017-05-09T17:57:04.646259:couldn't change working directory to "/oak/stanford/groups/russpold/data/ds000030_R1.0.3_analysis/sub-1
0624/bart/sub-10624_task-bart_bold_space-MNI152NLin2009cAsym_preproc_smooth.nii.gz": not a directory
170509-17:57:04,646 interface INFO:

         stderr 2017-05-09T17:57:04.646259:    while executing
170509-17:57:04,646 interface INFO:
         stderr 2017-05-09T17:57:04.646259:"cd $FD"
170509-17:57:04,646 interface INFO:
         stderr 2017-05-09T17:57:04.646259:    (procedure "firstLevelMaster" line 7)
170509-17:57:04,646 interface INFO:
         stderr 2017-05-09T17:57:04.646259:    invoked from within
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:"firstLevelMaster $session"
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:    invoked from within
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:"if { $done_something == 0 } {
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:    if { ! $fmri(inmelodic) } {
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:       if { $fmri(level) == 1 } {
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:           for { set session 1 } { $session <= $fmri(mult..."
170509-17:57:04,647 interface INFO:
         stderr 2017-05-09T17:57:04.646259:    (file "/usr/lib/fsl/5.0/feat" line 387)
Traceback (most recent call last):
  File "CNP_analysis.py", line 138, in <module>
    l1feat.run()
  File "/scratch/PI/russpold/crn-agave/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1043, in run
    runtime = self._run_wrapper(runtime)
  File "/scratch/PI/russpold/crn-agave/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1660, in _run_wrapper
    runtime = self._run_interface(runtime)
  File "/scratch/PI/russpold/crn-agave/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1694, in _run_interface
    self.raise_exception(runtime)
  File "/scratch/PI/russpold/crn-agave/anaconda/lib/python2.7/site-packages/nipype/interfaces/base.py", line 1618, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
feat /oak/stanford/groups/russpold/data/ds000030_R1.0.3_analysis/sub-10624/bart/run0.fsf
Standard output:

Standard error:
couldn't change working directory to "/oak/stanford/groups/russpold/data/ds000030_R1.0.3_analysis/sub-10624/bart/sub-10624_task-bart_bold_space-MN
I152NLin2009cAsym_preproc_smooth.nii.gz": not a directory
    while executing
"cd $FD"
    (procedure "firstLevelMaster" line 7)
    invoked from within
"firstLevelMaster $session"
    invoked from within
"if { $done_something == 0 } {

    if { ! $fmri(inmelodic) } {
       if { $fmri(level) == 1 } {
              for { set session 1 } { $session <= $fmri(mult..."
    (file "/usr/lib/fsl/5.0/feat" line 387)
Return code: 1
Interface FEAT failed to run.

[codecov-io]

Codecov Report

Merging #2000 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master    #2000   +/-   ##
=======================================
  Coverage   72.15%   72.15%           
=======================================
  Files        1117     1117           
  Lines       56456    56456           
  Branches     8112     8112           
=======================================
  Hits        40736    40736           
  Misses      14443    14443           
  Partials     1277     1277

Flag	Coverage Δ
#smoketests	72.15% <ø> (ø)	⬆️
#unittests	69.72% <ø> (ø)	⬆️

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[effigies]

Re-ran the tests. Passing now.