Re: [Freesurfer] Colortable in annotations

2010-04-13 Thread Nick Schmansky
i was going to have you link wm.mgz to T1.mgz as a hack to get mris_anatomical_stats to dump the colortable, but i see that mris_anatomical_stats complains about running against fsaverage. so rather than add a hack on a hack, i'll just update mris_info to dump the colortable of a .annot file.

Re: [Freesurfer] Colortable in annotations

2010-04-13 Thread Dankner, Nathan (NIH/NIMH) [F]
Thanks, that should be helpful. Is there a way to use mris_anatomical_stats on the .annot file that the cluster correction creates within the qdec analysis folder, or do I need to map the annotation to a subject in order to use mris_anatomical_stats? If I try to run mris_anatomical_stats on th

Re: [Freesurfer] Colortable in annotations

2010-04-09 Thread Dankner, Nathan (NIH/NIMH) [F]
Thanks, that should be helpful. Is there a way to use mris_anatomical_stats on the .annot file that the cluster correction creates within the qdec analysis folder, or do I need to map the annotation to a subject in order to use mris_anatomical_stats? If I try to run mris_anatomical_stats on th

Re: [Freesurfer] Colortable in annotations

2010-04-09 Thread Nick Schmansky
or you can use the -c option of mris_anatomical_stats to extract the colortable from the .annot file, edit the colors in that colortable, and then specify that colortable with the -colortable option of tksurfer. n. On Fri, 2010-04-09 at 14:49 -0400, Douglas N Greve wrote: > The only "easy" way to

Re: [Freesurfer] Colortable in annotations

2010-04-09 Thread Douglas N Greve
The only "easy" way to do it is to create individual labels for each cluster (using the label option or mri_annotation2label), then use mris_label2annot and specify your own color table. doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Hi all, > > I am running cluster corrections on data and attemp