Hi Doug, Yes, that's the file I referred to in my previous mail, I should have made that more clear. I'll take a look at the new label2vol, fortunately, I haven't run into the 999 limit yet. If you're re-coding it, it would be great if you could include an option to output the embedded colour table to a file, which would be less error-prone than hand-matching the correct colour tables (and would also work for files where you don't have the .ctab output, but only the embedded table). Thanks again, Johannes
Doug Greve schrieb:
There should be color tables in the stats directory, eg, stats/aparc.annot.a2005s.ctab
Also, there's a bug in label2vol that makes it fail on any segment with id > 999 (as the cortical ones in aparc+aseg are). I've put a new version at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol (already live in the NMR center).
You can also use mri_aparc2aseg to map the a2005s annot into the aseg volume (like aparc+aseg). I'm not sure what version you have, so I copied the most recent one into ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_aparc2aseg
Finally, mri_label2vol can be very slow. I'm almost finished with a version that is much faster.
doug
Johannes Klein wrote:
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