Dear Bruce, thank you so much for your reply; it seems to work now.
However, a weird thing, I also mentioned in my previous post, still happens: when using ic3 there are duplicate labels in the newly created annotations. > at least the following labelnames are given to two spatially separated > labels. > ic3.tri_vertex_25 (in fsaverage lh: cluster 1 around vertex 41132, cluster 2 > around vertex 157199) > ic3.tri_vertex_42 (in fsaverage lh: cluster 1 around vertex 137845, cluster 2 > around vertex 155417) Is there a way to avoid this? Thanks for your help, Franz Am 26.01.2012 um 14:47 schrieb Bruce Fischl: > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
