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 <fis...@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 <zkauf...@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 >> <fis...@nmr.mgh.harvard.edu <mailto: >> fis...@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 >> <fis...@nmr.mgh.harvard.edu <mailto: >> fis...@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. 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