Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum

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 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 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 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

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.