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 <gr...@nmr.mgh.harvard.edu> wrote: > 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
e0070_CC12_new.aseg.stats
Description: Binary data
_______________________________________________ Freesurfer mailing list 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.
