On Fri, Nov 27, 2015 at 3:58 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Genevieve

are you sure you are using the correct mri_cc? I used your command line and got 12 segments. How many segents do you get? It should generate segments numbered 230-241 I think. You'll need to make your own entries in the ColorLUT.txt file if you want to see them in prespecified colors and names and such

cheers
Bruce

On Fri, 27 Nov 2015, UQAM wrote:

Hi Zeke,
We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open
the aseg.12segmentsCC.mgz in a viewer.

Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments?
basically the mri_cc

Could you also please explain how to edit the ColorLut.txt file

Finally, what is the precise script of the mri_segstats to generate stats tables.

Thanks again,

Cheers,
Genevieve

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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent
to you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the sender
and properly
dispose of the e-mail.

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.