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 a valid statsfile". The files are indeed in the stats folder of subject e0042, but the default aseg.stats files are 8,5K and my CC_new.aseg.stats files are 4,5K. Hope it can help to solve the problem ; ) Genevieve * * * asegstats2table -i e0042/stats/e0042_CC12_new.aseg.stats e0041/stats/e0041_CC12_new.aseg.stats e0035/stats/e0035_CC12_new.aseg.stats e0048/stats/e0048_CC12_new.aseg.stats e0058/stats/e0058_CC12_new.aseg.stats e0059/stats/e0059_CC12_new.aseg.stats e0053/stats/e0053_CC12_new.aseg.stats e0032/stats/e0032_CC12_new.aseg.stats e0047/stats/e0047_CC12_new.aseg.stats e0036/stats/e0036_CC12_new.aseg.stats e0039/stats/e0039_CC12_new.aseg.stats e0049/stats/e0049_CC12_new.aseg.stats e0051/stats/e0051_CC12_new.aseg.stats e0050/stats/e0050_CC12_new.aseg.stats e0045/stats/e0045_CC12_new.aseg.stats e0061/stats/e0061_CC12_new.aseg.stats e0062/stats/e0062_CC12_new.aseg.stats e0063/stats/e0063_CC12_new.aseg.stats e0064/stats/e0064_CC12_new.aseg.stats e0065/stats/e0065_CC12_new.aseg.stats e0066/stats/e0066_CC12_new.aseg.stats e0067/stats/e0067_CC12_new.aseg.stats e0068/stats/e0068_CC12_new.aseg.stats e0070/stats/e0070_CC12_new.aseg.stats e0071/stats/e0071_CC12_new.aseg.stats e0072/stats/e0072_CC12_new.aseg.stats e0073/stats/e0073_CC12_new.aseg.stats e0074/stats/e0074_CC12_new.aseg.stats e0075/stats/e0075_CC12_new.aseg.stats e0076/stats/e0076_CC12_new.aseg.stats e0077/stats/e0077_CC12_new.aseg.stats e0021/stats/e0021_CC12_new.aseg.stats e0004/stats/e0004_CC12_new.aseg.stats e0078/stats/e0078_CC12_new.aseg.stats e0079/stats/e0079_CC12_new.aseg.stats e0080/stats/e0080_CC12_new.aseg.stats e0013/stats/e0013_CC12_new.aseg.stats e0081/stats/e0081_CC12_new.aseg.stats e0082/stats/e0082_CC12_new.aseg.stats e0083/stats/e0083_CC12_new.aseg.stats a0001/stats/a0001_CC12_new.aseg.stats a0002/stats/a0002_CC12_new.aseg.stats a0003/stats/a0003_CC12_new.aseg.stats a0004/stats/a0004_CC12_new.aseg.stats a0005/stats/a0005_CC12_new.aseg.stats a0006/stats/a0006_CC12_new.aseg.stats a0007/stats/a0007_CC12_new.aseg.stats a0008/stats/a0008_CC12_new.aseg.stats a0009/stats/a0009_CC12_new.aseg.stats a0010/stats/a0010_CC12_new.aseg.stats a0011/stats/a0011_CC12_new.aseg.stats a0012/stats/a0012_CC12_new.aseg.stats a0013/stats/a0013_CC12_new.aseg.stats a0014/stats/a0014_CC12_new.aseg.stats a0015/stats/a0015_CC12_new.aseg.stats a0016/stats/a0016_CC12_new.aseg.stats a0017/stats/a0017_CC12_new.aseg.stats a0018/stats/a0018_CC12_new.aseg.stats a0019/stats/a0019_CC12_new.aseg.stats a0020/stats/a0020_CC12_new.aseg.stats a0021/stats/a0021_CC12_new.aseg.stats a0022/stats/a0022_CC12_new.aseg.stats a0023/stats/a0023_CC12_new.aseg.stats a0024/stats/a0024_CC12_new.aseg.stats a0025/stats/a0025_CC12_new.aseg.stats a0026/stats/a0026_CC12_new.aseg.stats a0027/stats/a0027_CC12_new.aseg.stats a0028/stats/a0028_CC12_new.aseg.stats a0029/stats/a0029_CC12_new.aseg.stats a0030/stats/a0030_CC12_new.aseg.stats a0031/stats/a0031_CC12_new.aseg.stats a0032/stats/a0032_CC12_new.aseg.stats a0033/stats/a0033_CC12_new.aseg.stats a0034/stats/a0034_CC12_new.aseg.stats a0035/stats/a0035_CC12_new.aseg.stats a0036/stats/a0036_CC12_new.aseg.stats a0037/stats/a0037_CC12_new.aseg.stats a0038/stats/a0038_CC12_new.aseg.stats a0039/stats/a0039_CC12_new.aseg.stats a0040/stats/a0040_CC12_new.aseg.stats --meas volume --tablefile aseg_stats_12CC_new.txt On Tue, Dec 8, 2015 at 6:40 AM, UQAM <allaire-duquette.genevi...@uqam.ca> wrote: > 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 >> > >
_______________________________________________ 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.
