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

Can you send me one of the e0070_CC12_new.aseg.stats files?

On 12/06/2015 08:12 AM, UQAM wrote:

Hi Bruce,

We used these:

mri_cc_new -aseg aseg.auto_noCCseg.mgz -o aseg.12segmentsCC_new.mgz -d 12 e0070 ... (for all the subjects from e0042 to a0040)

mri_segstats --seg $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC_new.mgz --ctab $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid 0 --sum $SUBJECTS_DIR/e0070/stats/e0070_CC12_new.aseg.stats .... (for all the subjects from e0042 to a0040)

asegstats2table --subjects e0042 e0041 e0035 e0048 e0058 e0059 e0053 e0032 e0047 e0036 e0039 e0049 e0051 e0050 e0045 e0061 e0062 e0063 e0064 e0065 e0066 e0067 e0068 e0070 e0071 e0072 e0073 e0074 e0075 e0076 e0077 e0021 e0004 e0078 e0079 e0080 e0013 e0081 e0082 e0083 a0001 a0002 a0003 a0004 a0005 a0006 a0007 a0008 a0009 a0010 a0011 a0012 a0013 a0014 a0015 a0016 a0017 a0018 a0019 a0020 a0021 a0022 a0023 a0024 a0025 a0026 a0027 a0028 a0029 a0030 a0031 a0032 a0033 a0034 a0035 a0036 a0037 a0038 a0039 a0040 --meas volume --tablefile aseg_stats_12CC_new.txt

Genevieve

On Fri, Dec 4, 2015 at 5:56 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

HI Genevieve

you'll need to send us all your command lines


cheers
Bruce

On Fri, 4 Dec 2015, UQAM wrote:

    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
    <mailto: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 <mailto: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
    <mailto: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>
                            <mailto: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>
                            <mailto: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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