A 3dSkullStrip issue on Nipype 0.9.2

[Leemon Albert]

Hi, Nipype developers,

I've met a 3dSkullStrip issue with Nipype, using the code (with my costumed T1) form the Nipype document page.

from nipype.interfaces import afni as afni
skullstrip = afni.SkullStrip()
skullstrip.inputs.in_file = '/media/TOSHIBA_EXT/newdata2/cpac/work/resting_preproc_dp37_2/anat_preproc_0/anat_skullstrip/t1_resample.nii.gz'

1) skullstrip.inputs.args = '-o_ply'
res = skullstrip.run()

I aslo test the condition with the definition of outputtype and out_file.
2) skullstrip.inputs.args = '-o_ply'
skullstrip.inputs.outputtype = 'AFNI'
skullstrip.inputs.out_file = 'test'
res = skullstrip.run()

I could get the ply file and the skull-stripped NIFTI file in both cases.
However, the same FileNotFoundError, 'XXX + orig.BRIK' not found for SkullStrip output 'out_file', appeared in both.

One more thing, there is no error message if I run the same code in terminal.

---

140925-12:18:53,883 interface INFO:
stderr 2014-09-25T12:18:53.883272:The intensity in the output dataset is a modified version
140925-12:18:53,884 interface INFO:
stderr 2014-09-25T12:18:53.883272:of the intensity in the input volume.
140925-12:18:53,884 interface INFO:
stderr 2014-09-25T12:18:53.883272:To obtain a masked version of the input with identical values inside
140925-12:18:53,885 interface INFO:
stderr 2014-09-25T12:18:53.883272:the brain, you can either use 3dSkullStrip's -orig_vol option
140925-12:18:53,885 interface INFO:
stderr 2014-09-25T12:18:53.883272:or run the following command:
140925-12:18:53,886 interface INFO:
stderr 2014-09-25T12:18:53.883272: 3dcalc -a /media/TOSHIBA_EXT/newdata2/cpac/work/resting_preproc_dp37_2/anat_preproc_0/anat_skullstrip/t1_resample.nii.gz -b test+orig -expr 'a*step(b)' \
140925-12:18:53,886 interface INFO:
stderr 2014-09-25T12:18:53.883272: -prefix test_orig_vol
140925-12:18:53,887 interface INFO:
stderr 2014-09-25T12:18:53.883272:to generate a new masked version of the input.

---

FileNotFoundError Traceback (most recent call last)
/home/fmri/ in ()
5 skullstrip.inputs.outputtype = 'AFNI'
6 skullstrip.inputs.out_file = 'test'
----> 7 res = skullstrip.run()

/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.pyc in run(self, **inputs)
957 try:
958 runtime = self._run_interface(runtime)
--> 959 outputs = self.aggregate_outputs(runtime)
960 runtime.endTime = dt.isoformat(dt.utcnow())
961 timediff = parseutc(runtime.endTime) - parseutc(runtime.startTime)

/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.pyc in aggregate_outputs(self, runtime, needed_outputs)
1051 msg = ("File/Directory '%s' not found for %s output "
1052 "'%s'." % (val, self.class.name, key))
-> 1053 raise FileNotFoundError(msg)
1054 else:
1055 raise error

FileNotFoundError: File/Directory '/home/fmri/test+orig.BRIK' not found for SkullStrip output 'out_file'. Interface SkullStrip failed to run.

Any comments are appreciated.
Thanks
Meng

[Satrajit Ghosh]

hi meng,

could you please try this with the current master branch of nipype?

cheers,

satra

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[Leemon Albert]

Hi Satra,

Thanks for your suggestion.  I am not sure about this.Because I need the custom branch, NIPYPE-CPAC.

But after reinstalling the AFNI, the error message is changed as follows.

     ['Node anat_skullstrip failed to run on host fmri-Canlab.']
140926-10:22:27,460 workflow INFO:
     Saving crash info to /media/TOSHIBA_EXT/newdata2/cpac/log/crash-20140926-102227-fmri-anat_skullstrip.pklz
140926-10:22:27,460 workflow INFO:
     Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/plugins/multiproc.py", line 18, in run_node
    result['result'] = node.run(updatehash=updatehash)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1390, in run
    self._run_interface()
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1500, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/local/lib/python2.7/dist-packages/nipype/pipeline/engine.py", line 1626, in _run_command
    result = self._interface.run()
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 958, in run
    runtime = self._run_interface(runtime)
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1401, in _run_interface
    self.raise_exception(runtime)
  File "/usr/local/lib/python2.7/dist-packages/nipype/interfaces/base.py", line 1331, in raise_exception
    raise RuntimeError(message)
RuntimeError: Command:
3dSkullStrip -input /media/TOSHIBA_EXT/newdata2/cpac/work/resting_preproc_dp37_2/anat_preproc_0/anat_skullstrip/t1_resample.nii.gz -prefix t1_resample_skullstrip
Standard output:

Standard error:
No protocol specified
No protocol specified
freeglut (3dSkullStrip): failed to open display ':1'

Return code: 1

Interface SkullStrip failed to run.

Best

Meng

[Satrajit Ghosh]

hi leemon,

that error might be related to ssh-ing in to a requirement in afni to have a display. you will need to either install xvfb or ssh in with X support.

regarding your original error, if you can't use nipype directly, you might be better off asking that question on the cpac mailing list. i don't know what changes they have made to the custom version.

cheers,

satra