[pymvpa] Surface-based Searchlight?

[Matthias Ekman]

Nick, thank you so much! It's totally clear now.

I also saw that the PR got recently merged into master. Very muck looking
forward to testing/trying these new functions. Again, this is really a
great addition to PyMVPA. Very happy to see this being available. Cool
stuff! :)

Best,
 Matthias


On Fri, Nov 29, 2013 at 5:42 PM, Nick Oosterhof <nikolaas.oosterhof at unitn.it
> wrote:

> Hi Matthias,
>
> On Nov 29, 2013, at 6:17 AM, Matthias Ekman wrote:
>
> >> 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!
>
> You're welcome :-)
>
> >>> 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.
> >>
> > 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?
>
> Almost:
>
> - the options '-a' and '-e' are mutually exclusive. In the latter case
> (after aligning EPI to T1) you can use either '-e' or '-a', but not both.
> - note that you can also coregister the T1 to the EPI (so that the T1 is
> transformed, not the EPI). Also then you can use '-e' or '-a'.
> - assuming you have a good EPI image you can actually skip the T1-EPI
> coregistration step (step 2 you mentioned above) and run it with just '-e'.
> It well then take the anatomical from FS's recon-all and the output dir
> will have an anatomical (with suffix al2exp - "aligned to experimental
> volume") that is aligned to the EPI. This may be the preferred usage.
>
> Also:
> - I recently added experimental support for images in template space
> (MNI/Talairach) - but this has only been tested properly with anatomical
> images ('-a'), not EPIs ('-e'). So in that case EPI-T1 alignment should be
> done manually.
> - Always make sure to check the alignment visually. Usually the '_e3'
> files from AFNI's @AddEdge (generated by pymvpa2-prep-afni-surf) are most
> suitable for this. The latest version of the script should also generate a
> few "qa*.png" bitmap images that should help in inspecting the alignment.
>
> Please let me know if you have further questions.
>
> best,
> Nick
> _______________________________________________
> Pkg-ExpPsy-PyMVPA mailing list
> Pkg-ExpPsy-PyMVPA at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/pkg-exppsy-pymvpa/attachments/20131203/ec58706a/attachment.html>