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
On 06/23/2015 10:13 AM, Napolitano Antonio wrote:
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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--
Dr. Martin Reuter
Instructor in Neurology
Harvard Medical School
Assistant in Neuroscience
Dept. of Radiology, Massachusetts General Hospital
Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
Computer Science and Artificial Intelligence Lab,
Dept. of Electrical Engineering and Computer Science,
Massachusetts Institute of Technology
A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
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reu...@mit.edu
Web : http://reuter.mit.edu
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