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 _______________________________________________ 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.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
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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.