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.eduhttps://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.
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