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

Hi again Bruce,

The mri_cc & mri_segstats run just fine. - When I open the open the new segmented .mgz files (aseg.12segmentsCC_new.mgz) in tkmedit I can clearly visualize the 12 segments. - When I open the .stats file I get volumes for each of the 12 corpus callosum segments.

However, when I run the asegstats2table the result is a .txt file with the usual 5 segments of the corpus callosum (anterior, ...).

Any clue why the asegstats2table doesn't take into account the new 12 segments?

See relevant files attached,

As usual thanks so much ; ) Genevieve

On Fri, Dec 4, 2015 at 3:07 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Genevieve

I just reran it locally and confirmed that the segments start at 230 for me, so I'm not sure what's going on. Still, maybe it meets your needs for now (but be aware that when we release V6 the segment numbering is likely to start at 230)

cheers Bruce

On Fri, 4 Dec 2015, UQAM wrote:

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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