Can you send me one of the e0070_CC12_new.aseg.stats files? On 12/06/2015 08:12 AM, UQAM wrote: > 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 <mailto: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 > <mailto: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 <mailto: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 > <mailto: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> > <mailto: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> > <mailto: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> > > <mailto: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> > <mailto: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 > > > > > _______________________________________________ > 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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