Hi Matt, this means that those annotation are empty (ie, have no vertices with that label). Is this the case? Can you verify that those labels actually exist for this subject?
doug
On 08/10/2012 03:32 PM, mnd12@nmr.mgh.harvard.edu wrote:
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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer