[pymvpa] Surface-based Searchlight?

[Matthias Ekman]

Thanks a lot Yarik and Nick!

> I'm currently trying to convert my Freesurfer (FS) surfaces to afni; the
> provided scrip ``prep_afni_surf`` is very helpful.
>
> I assume you refer to pymvpa2-prep-afni-surf wrapper script in the PyMVPA
> bin directory?
>
> (There is a module lib_prep_afni_surf in mvpa2/support/afni that provides
> the actual implementation, but it is preferred to use this through the
> wrapper script).
>
> Also please note that the most recent code is available here:
> https://github.com/nno/PyMVPA



Thanks for the link to the most recent code! Yes indeed, I was referring to
the ``pymvpa2-prep-afni-surf`` wrapper script.



> > 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)?
>
> You can coregister surfaces to either an anatomical or EPI image ('-a' or
> '-e' options). If you have both, you should coregister them yourself, for
> example using AFNI's align_epi_anat.py.
>
> If you analyze data in original (not template) space, one option is to
> coregister anatomical files and surfaces to the EPI image. This reduces the
> amount of interpolation applied to the EPI image.



Just to make sure I really understand the difference between the -e/-a
options. In case I want to perform the SL analysis in the native EPI space
I'd follow these steps:

1. Freesurfer/recon-all based on the T1 anat
2. coregister T1 to the EPI using e.g ``align_epi_anat.py``
3. use the following command (using only "-e")

    pymvpa2-prep-afni-surf -s SUBJ_ID -d fs/surf/ -e func/func.nii.gz -r
OUTPUT_DIR -l 4

whereas if I coregister my EPI to the T1, I would use this command (using
"-e" and "-a")

    pymvpa2-prep-afni-surf -s SUBJ_ID -d fs/surf/ -a anat/anat.nii.gz -e
func/func.nii.gz -r OUTPUT_DIR -l 4

Is that correct? If not what would be the correct command/sequence in that
case?


> > 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.
>
> AFNI provides 3dVol2Surf and 3dSurf2Vol to transform results between
> volume and surfaces.
>

Ah, perfect. That does the trick.


Thanks a lot!
 Matthias



> best,
> Nick
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