[pymvpa] Issues with prep-afni-surf (for surface-based searchlights)

[Mike E. Klein]

Hi all,

I’m attempting to use pymvpa2-prep-afni-surf to preprocess my freesurfer
data before running surface searchlights. As I can’t get AFNI/SUMA
installed on my Mavericks osx system, I’m doing this all through VMware and
NeuroDebian (with PyMVPA and AFNI/SUMA installed).

I believe I’m following the instructions correctly, but get error messages
that I can’t interpret. I’ve pointed the script toward a 3D example
functional image, the freesurfer directory for a specific subject, and an
empty folder for output. Any advice would be appreciated! Messages are
below.

Best,
Mike

—

brain at neurodebian:~/host/april_analyses/subs$ pymvpa2-prep-afni-surf -e
05/warps/example_func.nii -d surfer/05/surf/ -r 05/prepper/
> Namespace(AddEdge='yes', aea_opts='-cmass cmass+xyz -big_move',
anatvol=None, epivol='05/warps/example_func.nii', expvol=None,
expvol_ss='yes', hemi='l+r', identity=False, isepi=None,
ld='4+8+16+32+64+128', notemplate=False, overwrite=False,
refdir='05/prepper/', sid=None, steps='all', surfdir='surfer/05/surf/',
surfformat='ascii', template=False)
Looking in
/media/sf_host/april_analyses/subs/surfer/05/surf/../scripts/recon-all.done
Found Freesurfer sid 05
Set absolute path for expvol:
/media/sf_host/april_analyses/subs/05/warps/example_func.nii
Set absolute path for refdir: /media/sf_host/april_analyses/subs/05/prepper
Set absolute path for surfdir:
/media/sf_host/april_analyses/subs/surfer/05/surf
/bin/sh: 1: 3dAttribute: not found
Traceback (most recent call last):
  File "/usr/bin/pymvpa2-prep-afni-surf", line 25, in <module>
    run_prep_afni_surf(vars(d))
  File
"/usr/lib/pymodules/python2.7/mvpa2/support/afni/lib_prep_afni_surf.py",
line 1205, in run_prep_afni_surf
    augmentconfig(config)
  File
"/usr/lib/pymodules/python2.7/mvpa2/support/afni/lib_prep_afni_surf.py",
line 266, in augmentconfig
    outvol_space = utils.cmd_capture_output(cmd)
  File "/usr/lib/pymodules/python2.7/mvpa2/support/afni/afni_utils.py",
line 123, in cmd_capture_output
    return subprocess.check_output(cmd, env=env, shell=True)
  File "/usr/lib/python2.7/subprocess.py", line 544, in check_output
    raise CalledProcessError(retcode, cmd, output=output)
subprocess.CalledProcessError: Command '3dAttribute TEMPLATE_SPACE
/media/sf_host/april_analyses/subs/05/warps/example_func.nii' returned
non-zero exit status 127
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