does it work if you don't use --maxstatwinner ? On 05/13/2015 05:31 PM, Aaron Goldman wrote: > Hello, > > >From the standard "fsaverage" subject, I'm trying to map a series of > labels (?h.oasis.chubs.*) to a group of my own subjects. My end goal > is to create summary files equivalent to ?h.aparc.stats for each > subject. For sample commands, I've been looking at the "BA label" > section of a subject's recon-all.log > > For my test subject, I first ran mris_label2label on each of the seven > regions for each hemisphere, and then I visually confirmed that the > labels were generated correctly. Here's an example of those commands: > > mri_label2label --srcsubject fsaverage --srclabel > $FREESURFER_HOME/subjects/fsaverage/label/lh.oasis.chubs.ifc.label > --trgsubject $subj --trglabel > $SUBJECTS_DIR/$subj/label/lh.oasis.chubs.ifc.label --hemi lh > --regmethod surface > > However, I ran into trouble when I tried to combine the labels into an > annotation file. This is the command I'm using: > > cd $subj/label > mris_label2annot --s $subj --hemi $hemi --ctab > ~/colortable_oasis.chubs.txt --l lh.oasis.chubs.ifc.label --l > lh.oasis.chubs.ipc.label --l lh.oasis.chubs.ips.label --l > lh.oasis.chubs.lateraltemporal.label --l > lh.oasis.chubs.medialpfc.label --l lh.oasis.chubs.mtl.label --l > lh.oasis.chubs.retrosplenial.label --l lh.oasis.chubs.tp.label --a > oasis.chubs --maxstatwinner --noverbose > > And these are the contents of colortable_oasis.chubs.txt, which I > created by modifying /usr/local/freesurfer/average/colortable_BA.txt: > > 0 unknown 25 5 25 0 > 1 oasis.chubs.ifc 0 92 23 0 > 2 oasis.chubs.ipc 131 148 255 0 > 3 oasis.chubs.ips 0 0 255 0 > 4 oasis.chubs.lateraltemporal 255 102 51 0 > 5 oasis.chubs.medialpfc 196 255 20 0 > 6 oasis.chubs.mtl 255 51 204 0 > 7 oasis.chubs.retrosplenial 1 38 153 0 > 8 oasis.chubs.tp 153 0 38 0 > > The problem is, when I inspect the annotation file, I'm ending up with > the entire brain labeled "unknown". Any ideas what I'm doing wrong? > > Thanks, > > Aaron > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
