Hi Genevieve
I just tracked this down and it is a bug in mri_cc. If you tell Zeke your hardware/software environment he can get you a new version that should work
cheers
Bruce
On Mon, 23 Nov 2015, UQAM wrote:
Hi Bruce,
Please find the two files attached.
Genevieve
On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Geneviève
if you send us the $SUBJECTS_DIR/CColorLUT.txt and $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a
look
cheers
Bruce
On Mon, 23 Nov 2015, UQAM wrote:
Hi,
This a a "re-posting" of a question I've raised last week ; )
I would like to segment the corpus callosum into twelve even lenght segments
instead of the five segments that freesurfer includes 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
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