[pymvpa] Surface-based Searchlight?

[Yaroslav Halchenko]

Hi Matthias,

Nick (the author of 119) is traveling atm, so there might be a delay
with the answer and I better defer to nick to give a complete answer.

meanwhile I would encourage anyone interested to their capacity go
through the changes in that PR
https://github.com/PyMVPA/PyMVPA/pull/119/files
and help us along with the review  ;)

On Thu, 28 Nov 2013, Matthias Ekman wrote:

>    Hi,
>    it seems that upcoming pymvpa2 release is going to include a long list of
>    exciting new features including Surface-based searchlight analysis.�
>    While still under development [1] I couldn't wait but having a first look.
>    I hope you guys don't mind me asking some simple questions.
>    I'm currently trying to convert my Freesurfer (FS) surfaces to afni; the
>    provided scrip ``prep_afni_surf`` is very helpful.
>    However, in my case it fails as recent FS (v5.3) doesn't seem to produce
>    the
>    COR files anymore? ("grep: COR-.info: No such file or directory"). Running
>    ``@SUMA_Make_Spec_FS`` with the "-use_mgz" flag however works. Maybe this
>    is a more sensible default, as the FS wiki marks COR as deprecated [2].�
>    Q1: Do I understand correctly that the EPI image must be coregistered to
>    the anatomical before running ``prep_afni_surf`` (i.e. afni is not doing
>    that 'magically' otherwise)?
>    Q2: How would one save/transform the results back to a volume format? E.g.
>    the ``fn = 'ico%d-%d_%sh_%dvx.niml.dset' % (lowres_ld, highres_ld, hemi,
>    radius)`` in the surface-based Searchlight example [3]. Afni seems to have
>    "3dAFNItoNIFTI" but that doesn't seem to work with SUMA files; I'm a bit
>    lost here.
>    Thanks in advance,
>    �Matthias
>    [1]�[1]https://github.com/PyMVPA/PyMVPA/pull/119
>    [2]�[2]http://freesurfer.net/fswiki/FsTutorial/CorFormat
>    [3]�[3]http://www.pymvpa.org/examples/searchlight_surf.html

> References

>    Visible links
>    1. https://github.com/PyMVPA/PyMVPA/pull/119
>    2. http://freesurfer.net/fswiki/FsTutorial/CorFormat
>    3. http://www.pymvpa.org/examples/searchlight_surf.html

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-- 
Yaroslav O. Halchenko, Ph.D.
http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
Senior Research Associate,     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