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

[Mike E. Klein]

Thanks, got it now on my native OSX.


On Sat, May 10, 2014 at 8:20 PM, Yaroslav Halchenko
<debian at onerussian.com>wrote:

>
> 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
>
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