Hi Geneviève
did the mri_cc step work? Looking at the code it (inexplicably) limits the max # of divisions to 5. I'm surprised it didn't segfault. If that part worked I defer to Doug on the rest, but if not we can send you a new mri_cc that should fix the problem
cheers Bruce
On Wed, 18 Nov 2015, UQAM wrote:
Hi, I would like to segment the corpus callosum into twelve even lenght segments instead of the five segments that freesurfer identifies by default.
- First I ran a mri_cc on subject e0070:
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC.mgz -d 12 e0070
- Then I edited the ColorLUT.txt file and renamed it CColorLUT.txt (see
attachment, segments 251 to 262).
- Finally I ran a mri_segstats to compute the statistics on segmented
volumes.
mri_segstats seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 sum --e0070_CC12.aseg.stats
The e0070_CC12.aseg.stats file still displays only five segments of the corpus callosum.
Any tips or clues on how I could do things differently to get 12 segments?
Thanks in advance,
Geneviève