I don't think it should be as long as you are consistent. It might be worth trying to track down this problem just so that you don't have to mix versions. doug
On 11/20/2012 03:37 PM, Berg, S.F. van den wrote: > Hi Doug, > > Thanks for respons. We also install the dev version of freesurfer. We do the > recon-all with the stable version. But smoothing with the dev version. Qdec > is till now on correctly running with the dev version. > > Running qDEC with the dev version. Is that a problem? > > Thanks, > > Stan > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: 20 November 2012 21:04 > To: Berg, S.F. van den > Subject: Re: [Freesurfer] error in analyze command failed: mri_concat > > If you change the order or leave one out, does it still crash? > > On 11/19/2012 11:21 AM, Berg, S.F. van den wrote: >> Hi Doug, >> >> I try the mri_concat command with the --debug flag. Output is also in the >> text file >> >> Thanks. >> >> Stan >> >> -------- freesurfer-Linux-centos5_x86_64-dev-20110315 -------- >> SUBJECTS_DIR /data1/projects/ysbrand-vumc/pddatabase-freesurfer >> guest@somerenserver:~$ mri_concat --debug >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >> >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >> --o >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh11 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >> 10 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >> 9 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >> 8 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >> 7 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >> 6 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >> 5 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >> 4 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >> 3 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >> 2 --o >> ninputs = 9 >> Checking inputs >> Checking 0 >> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >> reading MRI_FRAME structure from file... >> Segmentation fault >> >> >> ________________________________________ >> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] >> Sent: 19 November 2012 16:50 >> To: Berg, S.F. van den >> Subject: Re: [Freesurfer] error in analyze command failed: mri_concat >> >> Hi Stan, can you run it again this time with --debug as the first >> argument and send me the result? >> thanks >> doug >> >> On 11/19/2012 08:00 AM, Berg, S.F. van den wrote: >>> Hi Doug, >>> >>> Like you said. I run the command in the terminal. >>> >>> I run the mri_concat command with 9 subjects in the command line. for the >>> LH thickness and volume. A segmentation fault is the problem. >>> >>> What do i have to do in this case? >>> >>> Many thanks, >>> Stan >>> >>> -------- freesurfer-Linux-centos5_x86_64-dev-20110315 -------- >>> SUBJECTS_DIR /data1/projects/ysbrand-vumc/pddatabase-freesurfer >>> guest@somerenserver:~$ mri_concat >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >>> --o >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> ninputs = 9 >>> Checking inputs >>> reading MRI_FRAME structure from file... >>> Segmentation fault >>> guest@somerenserver:~$ mri_concat >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.thickness.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.thickness.fwhm10.fsaverage.mgh >>> --o >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/caudalmiddlefrontal_curv/y.mgh >>> ninputs = 9 >>> Checking inputs >>> reading MRI_FRAME structure from file... >>> Segmentation fault >>> guest@somerenserver:~$ >>> >>> >>> ________________________________________ >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >>> [gr...@nmr.mgh.harvard.edu] >>> Sent: 13 November 2012 17:32 >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] error in analyze command failed: mri_concat >>> >>> Hi Stan, can you run that mri_concat command from the terminal command line >>> and send me the resulting terminal output? I've put the command below >>> >>> doug >>> >>> mri_concat >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >>> --o >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> >>> >>> >>> On 11/13/2012 06:53 AM, Berg, S.F. van den wrote: >>>> mri_concat >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >>>> >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >>>> --o >>>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> -- >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> _______________________________________________ >>> 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. >>> >>> -------------------------------------------------------------------------------------------------------------- >>> >>> Mail 13 november 2012: >>> >>> Hello Freesurfer experts, >>> I have got some problems with qdec. For testing my data i make an design >>> with age, sexe and right and left hippocampus. The same design as the >>> tutorial on the freesurfer wiki. When starting analyze i get an Error in >>> Analyze: command failed: mri_concat >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh. >>> surf is the map with the smoothings. The correct smoothings file. In this >>> design is 10 is correctly presented in the map surf. >>> Thanks, >>> Stan >>> >>> lh-Avg-Intercept-volume ----------------------- >>> Does the average volume differ from zero? >>> 1.000 1.000 0.000 0.000; >>> lh-Avg-volume-Left-Hippocampus-Cor ----------------------- >>> Does the correlation between volume and Left-Hippocampus, accounting for >>> gender, differ from zero? >>> 0.000 0.000 1.000 1.000; >>> lh-Diff-male-female-Intercept-volume ----------------------- >>> Does the average volume differ between male and female? >>> 1.000 -1.000 0.000 0.000; >>> lh-Diff-male-female-Cor-volume-Left-Hippocampus ----------------------- >>> Does the volume--Left-Hippocampus correlation differ between male and >>> female? >>> 0.000 0.000 1.000 -1.000; >>> ninputs = 9 >>> Checking inputs >>> reading MRI_FRAME structure from file... >>> Error in Analyze: command failed: mri_concat >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0050/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0051/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0054/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0060/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0062/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0064/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0067/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0075/surf/lh.volume.fwhm10.fsaverage.mgh >>> >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/0080/surf/lh.volume.fwhm10.fsaverage.mgh >>> --o >>> /data1/projects/ysbrand-vumc/pddatabase-freesurfer/qdec/hippocampus/y.mgh >>> >>> >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- 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: 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
