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 <[email protected] > 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 > [email protected] > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/pkg-exppsy-pymvpa >
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