Hi Doug, Thanks for the file. Unfortunately, it doesn't do the trick. I went back to the log file which reads
colortable with 82 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild/Simple_surface_labels2005.txt)
Saving annotation colortable ../stats/aparc.annot.a2005s.ctab
D'uh ... should have read this more patiently before - I had just looked for simple_surface_labels2005.txt and not read on ;)
Out of curiosity, is there a way to extract a colour table from an annot file? Thanks again, Johannes
Doug Greve schrieb:
Try using the one in:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/FreeSurferColorLUT.txt
doug
Johannes Klein wrote:
Hi folks, I'd like to create a volume segmentation from Freesurfer's .annot output. I can get it back into volume land with something like
mri_label2vol --subject sub1 --annot ../label/lh.aparc.a2005s.annot --o sub1_parcellated.mgz --hemi lh --temp norm.mgz --proj frac 0 1 0.1
The thing I'm missing, though, is the appropriate colour table - I don't know how to extract the embedded one from lh.aparc.a2005s.annot I loaded the result into tkmedit and tried the different colour tables (my best bet being surface_labels.txt) provided, but none of them gives correct anatomical labels. Thanks for your help everyone, Johannes _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer