Hi Martin and Bruce,
Thanks for your replies!
I thought, maybe I am wrong, that a reference subject could be the best choice
for my purposes.
however, in principle, can I do the same procedure as you described for my
reference subject as well?
or similarly, can I use MNI standard surface, creating the annot file I desire
and going for mri_surf2surf to get the mapping on each subject?
Best wishes
Antonio
Hi Antonio,
why not draw your labels on fsaverage, and then map them to each subject (look
at mri_surf2surf or mri_label2label, mri_segstats ). In my opinion you don't
need the do all the registration of volumes, you only work on surfaces.
Probably someone here can give you the exact commands for creating an
annotation, mapping it to the subjects and computing stats.
Best, Martin
Hi Antonio
if you want the parcels to be in register you should use the sphere.reg instead
of the sphere file in mris_make_face_parcellation.
I'll leave the other questions for Doug:)
Bruce
________________________________
Da: Napolitano Antonio
Inviato: martedì 23 giugno 2015 16.13
A: freesurfer@nmr.mgh.harvard.edu
Oggetto: cortical parcelling with freesurfer
Dear freesurfer experts,
I am having few questions about using freesurfer to finely (1000) parcel
cortical structures consistently through subjects.
Since I cannot do GCs atlas on my own, the main idea is running recon_all for
all of them and then register via mri_cvs_register all subjects to one; first
question: shall I run bbregister before mri_cvs_register or the latter will
take care of everything?
Once I have done that I do parcel the cortical stuff in the reference subject
by using the command:
mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid}/surf/lh.sphere
${FREESURFER_HOME}/lib/bem/ic3.tri ${SUBJECTS_DIR}/${subjid}/label/lh.ic3.annot
I am not sure if that is correct...any hints will be very appreciated.
After that I am facing the problem of translating the lh.ic3.annot to the
surface of each subject in his original space; running mri_cvs_register I get
two resampled pial (lh.resample.pial and lh.dbg_surf.pial: I am not sure which
one must be used and I am not sure what is the difference between them), but
how can I get the parcellation back to the space of each suject? Mri_vol2vol
seems to be working with volumes only whereas I would need to apply the m3z to
surfaces. Shall I convert the annot to label and then to volumes so that I can
apply the warping directly to the volumes or is there a shortcut way to do so?
I am little bit stack at the moment and I would really thankful for any help or
suggestions.
Best Wishes
Antonio
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