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 5 250
1 oasis.chubs.ifc 0 92 230
2 oasis.chubs.ipc 131 148 2550
3 oasis.chubs.ips 0 0 2550
4 oasis.chubs.lateraltemporal 255 102 510
5 oasis.chubs.medialpfc 196 255 200
6 oasis.chubs.mtl 255 51 2040
7 oasis.chubs.retrosplenial 1 38 1530
8 oasis.chubs.tp 153 0 380
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
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