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

Hi Doug, Hi Bruce, Just an update. I tried this command (see below) to specify each input file since I don't want to freesurfer to choose the stats/aseg.stats that it uses by default. but I get this "ERROR: The stats file e0042/stats/e0042_CC12_new.aseg.stats is not found or is too small to be

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

Hi Doug, See attached an example of an aseg.stats file for subject e0070 ( e0070_CC12_new.aseg.stats) Regards, Genevieve On Mon, Dec 7, 2015 at 7:48 PM, Douglas N Greve wrote: > Can you send me one of the e0070_CC12_new.aseg.stats files? > > On 12/06/2015 08:12

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

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

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

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

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

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

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

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

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

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

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

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

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

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 wrote: > Hi Genevieve > > I just tracked this down and it is a bug in mri_cc. If you

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

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,

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

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