Hello,
I'm attempting to use a custom parcellation scheme (Lausanne2008) on fsaverage5. The gcs files I'm using can be found here:
https://github.com/LTS5/cmp/tree/master/cmp/data/colortable_and_gcs/my_atlas...
The problem I'm getting is when I run mri_annotation2label using the annotation files I create using these gcs files and lh.sphere.reg I noticed that some of the labels are not being extracted, as seen in the first few lines of output copy/pasted here:
0 820 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.unknown.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.unknown.label 4 190 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.corpuscallosum.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.corpuscallosum.label 6 30 /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.entorhinal_1.label LabelWrite: saving to /autofs/cluster/neuromind/matt/fsaverage5/FSaverage5/tp1/FREESURFER/label/regenerated_lh_500/lh.entorhinal_1.label
so it appears to skip labels 1,2,3 and 5. Interestingly this problem is only occurring when I use the gcs files named P1_16 P17_28 P29_36. Also, I'm able to successfully use this parcellation scheme on other subjects and with fsaverage, just not fsaverage5. Any help would be greatly appreciated!
Thanks in advance, Matt DeSalvo