On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman@nmr.mgh.harvard.edu> wrote:

Hello Genevieve,

Below is a link to the newest version of mri_cc. Please copy it to your FREESURFER_HOME directory and backup the original.

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc

Hope this help.

-Zeke

On 11/24/2015 05:56 AM, UQAM wrote:

Hi Bruce,

DELL R910
Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores)
32 Go RAM
CentOS release 5.10 (Final)
kernel 2.6.18-371.3.1.el5

On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote:

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 <mailto: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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