Hi Franz looks like this was a bug in mris_make_face_parcellation, which I just fixed. It was always using the sphere regardless of what you specified. Krish: can you get Franz a new mac version of it to try out?
sorry Bruce On Thu, 26 Jan 2012, Franz Liem wrote: > Dear Freesurfers, > > I have some questions regarding mris_make_face_parcellation (and possibly > found one error in the .tri file). > (I am working with freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0). > > I would like to make a high res parcellation of several subjects and used > ic3.tri. Parcels should correspond across subjects. > I computed mris_make_face_parcellation ../surf/lh.sphere > $FREESURFER_HOME/lib/bem/ic3.tri ./lh.ic3.annot > > 1. It seems not to make a difference whether I choose .sphere or .sphere.reg > as input, the resulting parcellations are identical (i checked by comparing > vertex label values in matlab; .inflated deviates a bit, but not > substantially). > According to Bruce > (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18509.html): > "You want to use either ?h.sphere if you want it to be uniform in subject > space or ?h.sphere.reg if you want the parcels to correspond across subjects" > > Could anybody tell me how the parcellation is performed exactly? I thought it > was performed on the input surf (the input surf is parcellated into (e.g.) > 642 equally sized parcels), which should lead to different results at .sphere > and .sphere.reg, shouldn't it? > > Alternatively, would it be better to mris_make_face_parcellation the > fsaverage and mri_surf2surf the high res parcellation onto each subject to > get cross-subject correspondency (I tried this. It didn't look that great > with this command: mri_surf2surf --srcsubject fsaverage --sval-annot > ic3.annot --trgsubject subject1 --tval ic3s03.annot --hemi lh )? > > To recap, what is the best strategy to arrive with cross-subject-corresponing > parcellations? Performing mris_make_face_parcellation with ?h.sphere.reg for > each subject individually? > > 2. There seems to be duplicate structNames/annotationValues when applying > mris_make_face_parcellation with ic3.tri > In fsaverage at least the following labelnames are given to two spatially > separated labels. > ic3.tri_vertex_25 (cluster 1 around vertex 41132, cluster 2 around vertex > 157199) > ic3.tri_vertex_42 (cluster 1 around vertex 137845, cluster 2 around vertex > 155417) > How come? > > > Thanks for you help, > Franz > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ 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.
