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
Il tuo 5 per mille al Progetto ospedale senza dolore
Lavoriamo per il controllo del dolore nei bambini
e la diminuzione dell'ansia e dello stress nei genitori.
Ci aiuti anche tu?
Dona il tuo 5 X Mille
all'Ospedale Pediatrico Bambino Gesù
CF 80403930581 (sezione Ricerca Sanitaria)?
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
