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

Hi Bruce,

We were using the correct mri_cc, but our segments were numbered 251 to 262 instead of 230 to 241 in the CColorLUT.txt. With this adjustment, the mri_cc now runs perfectly and segments in 12.

Many thanks for your support!

Best, Genevieve

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


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