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

[Yaroslav Halchenko]

On Fri, 09 May 2014, Mike E. Klein wrote:

>    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

read between the lines! ;)   probably just 

source /etc/afni/afni.sh

before running pymvpa2-prep-afni-surf or altogether in your
~/.bashrc -- it seems that even if you said to source them when going
through the welcome wizard, they weren't :-/

-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Research Scientist,            Psychological and Brain Sciences Dept.
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik