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 <fis...@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 <fis...@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 < >> 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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