Hi Doug, I deleted all of the template.nii files, and now the command works. Thank you for your advice!
In regards to my other thread (selxavg3-sess error), where selxavg3 looks for a file that doesn't exist (fmcpr.sm5.nii.gz), could I rename the preproc-sess output volume (fmcpr.nii.gz) to fmcpr.sm5.nii.gz in order to run the command? Given preproc-sess at -fwhm 5, this volume should be smoothed at 5 and should be the input for analysis, correct? Thanks, Anais ________________________________________ From: [email protected] [[email protected]] on behalf of Douglas N Greve [[email protected]] Sent: Tuesday, August 04, 2015 3:08 PM To: [email protected] Subject: Re: [Freesurfer] Dimension mismatch between mask and run There is still a warning about "multiple formats". This means you have not deleted all the offending files. On 08/04/2015 12:19 PM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > Thanks for getting back to me. I tried deleting those files, and got the same > error, although the terminal output looked slightly different towards the end > (in terms of the compensation values). > > Here it is below: > -------------------------------------------------------------- > selxavg3-sess logfile is > /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150804121216.log > -------------------------------------------------------------- > preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a > SIRP_LoadRegression_Stable5_050514 -nolog > -------------------------------------------------------------- > preproc-sess logfile is /dev/null > -------------------------------------------------------------- > $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ > arodthom > setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 > setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun > Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 > x86_64 x86_64 x86_64 GNU/Linux > /autofs/cluster/roffman/users/Stable5_PerRun > /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess > -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a > SIRP_LoadRegression_Stable5_050514 -nolog > Tue Aug 4 12:12:17 EDT 2015 > instem f > mc 1 f fmcpr > stc 0 fmcpr > sm 0 fmcpr > mask 1 brain > GDDA098 Template ----------------------------- > mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun > -fsd bold -rlf runlistfile -nolog -update > > Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 ---------------- > Tue Aug 4 12:12:17 EDT 2015 > Detected input format at nii > GDDA098 Update not needed > Run: 015 ---------------- > Tue Aug 4 12:12:17 EDT 2015 > GDDA098 015 Update not needed > Run: 016 ---------------- > Tue Aug 4 12:12:17 EDT 2015 > GDDA098 016 Update not needed > Run: 017 ---------------- > Tue Aug 4 12:12:17 EDT 2015 > GDDA098 017 Update not needed > Tue Aug 4 12:12:17 EDT 2015 > mktemplate-sess completed > GDDA098 Mask ------------------------ > mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d > /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update > ------------------------------------------------ > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 > Tue Aug 4 12:12:17 EDT 2015 > WARNING: multiple formats found for template > USING: template.nii.gz > GDDA098 Update not needed for session-level mask > WARNING: multiple formats found for 015/template > USING: 015/template.nii.gz > GDDA098 Update not needed for run 015 mask > GDDA098 Update not needed for run 015 meanval > WARNING: multiple formats found for 016/template > USING: 016/template.nii.gz > GDDA098 Update not needed for run 016 mask > GDDA098 Update not needed for run 016 meanval > WARNING: multiple formats found for 017/template > USING: 017/template.nii.gz > GDDA098 Update not needed for run 017 mask > GDDA098 Update not needed for run 017 meanval > Tue Aug 4 12:12:18 EDT 2015 > mkbrainmask-sess done > GDDA098 Registration ----------------------------- > register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -fsd > bold -dof 6 -rlf runlistfile -per-run -nolog -update > -------------------------------------------------------------- > register-sess logfile is /dev/null > -------------------------------------------------------------- > Tue Aug 4 12:12:18 EDT 2015 > > setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun > cd /autofs/cluster/roffman/users/Stable5_PerRun > /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d > /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf > runlistfile -per-run -nolog -update > > cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or > directory > Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 > x86_64 x86_64 x86_64 GNU/Linux > > Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 ---------------- > Tue Aug 4 12:12:18 EDT 2015 > Run: 015 ---------------- > Tue Aug 4 12:12:18 EDT 2015 > WARNING: multiple formats found for bold/015/template > USING: bold/015/template.nii.gz > Update not needed > Run: 016 ---------------- > Tue Aug 4 12:12:18 EDT 2015 > WARNING: multiple formats found for bold/016/template > USING: bold/016/template.nii.gz > Update not needed > Run: 017 ---------------- > Tue Aug 4 12:12:18 EDT 2015 > WARNING: multiple formats found for bold/017/template > USING: bold/017/template.nii.gz > Update not needed > Tue Aug 4 12:12:18 EDT 2015 > register-sess completed > GDDA098 MC ----------------------------- > mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -d > /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile > -per-run -nolog -update > Logfile is /dev/null > ------------------------------------------- > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 > RunList: 015 016 017 > WARNING: multiple formats found for 015/template > USING: 015/template.nii.gz > GDDA098 015 Update not needed > WARNING: multiple formats found for 016/template > USING: 016/template.nii.gz > GDDA098 016 Update not needed > WARNING: multiple formats found for 017/template > USING: 017/template.nii.gz > GDDA098 017 Update not needed > > > Tue Aug 4 12:12:18 EDT 2015 > mc-sess completed SUCCESSFULLY > ---------------------------------------- > Started at Tue Aug 4 12:12:17 EDT 2015 > Ended at Tue Aug 4 12:12:18 EDT 2015 > preproc-sess done > ------------------------------------------- > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 > Tue Aug 4 12:12:19 EDT 2015 > anadir = > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 > DoGLMFit = 1 > DoContrasts = 1 > UpdateNeeded = 1 > ------------------------------------------ > ------- matlab output -------------------- > No window system found. Java option 'MWT' ignored. > Warning: Unable to open display 'iconic'. You will not be able to display > graphics on the screen. > Warning: No window system found. Java option 'MWT' ignored. > > < M A T L A B (R) > > Copyright 1984-2013 The MathWorks, Inc. > R2013b (8.2.0.701) 64-bit (glnxa64) > August 13, 2013 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > > sxa3pwd = > > /autofs/cluster/roffman/users/Stable5_PerRun > > sxa3cmd = > > /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -s GDDA098 > -analysis SIRP_LoadRegression_Stable5_050514 > >>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m > #@# GDDA098 ############################### > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 > ------------------------- > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m > /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_ldanaflac.m > /usr/local/freesurfer/stable5_3_0/matlab/MRIread.m > ------------------------- > outtop = /autofs/cluster/roffman/users/Stable5_PerRun > Extension format = nii.gz > 1 Cond2vFix.mat > Excluding 0 points > nruns = 3 > autostimdur = > > > outanadir = > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 > Excluding 0 points > Excluding 0 points > Excluding 0 points > Found 49193/143360 (34.3) voxels in mask > Creating Design Matrix > ... creation time = 0.011 sec > DoMCFit = 1 > ntptot = 705, nX = 18, DOF = 687 > Saving X matrix to > /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514/Xtmp.mat > XCond = 35.9364 (normalized) > Computing compensation for resdual AR1 bias > 1 -0.5 -0.507451 (t=0.046548) > 2 -0.25 -0.264 (t=0.105696) > 3 0 -0.0235997 (t=0.137308) > 4 0.25 0.211292 (t=0.189719) > 5 0.5 0.434363 (t=0.217673) > AR1 Correction M: 0.031657 1.0595 > Computing contrast matrices > OLS Beta Pass > run 1 t= 0.0 > ERROR: dimension mismatch between mask and 1th run >>> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > ________________________________________ > From: [email protected] > [[email protected]] on behalf of Douglas N Greve > [[email protected]] > Sent: Tuesday, August 04, 2015 11:39 AM > To: [email protected] > Subject: Re: [Freesurfer] Dimension mismatch between mask and run > > I'm not sure, but it may be that there are some files that are nii and > others that are nii.gz. Eg, > > ls -tl /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/015/masks/ > total 1248 > -rw-rw---- 1 arodthom roffmagp 3579 Aug 3 18:06 brain.e3.nii.gz > -rw-rw---- 1 arodthom roffmagp 5383 Aug 3 18:06 brain.nii.gz > -rw-rw---- 1 arodthom roffmagp 606560 Mar 16 11:02 brain.e3.nii > -rw-rw---- 1 arodthom roffmagp 606560 Mar 16 11:02 brain.nii > > The nii.gz are newer but I think selxavg3-sess will use the nii files, > which have probably not been updated. Try deleting the same-named nii files > > > On 08/03/2015 06:32 PM, Rodriguez-Thompson, Anais wrote: >> Hi Freesurfer experts, >> >> For a data set of n=100, selxavg3 is erroring out on 10 subjects (GDDA086, >> 88, 89, 91, 93, 94, 95, 96, 97, and 98). It says ERROR: dimension mismatch >> between mask and 1th run. Do you know why freesurfer is having trouble with >> these subjects in particular, and how I can avoid this error? >> >> Thanks for your help, >> Anais >> >> Below is the terminal window output: >> -------------------------------------------------------------- >> selxavg3-sess logfile is >> /autofs/cluster/roffman/users/Stable5_PerRun/log/selxavg3-sess-bold-SIRP_LoadRegression_Stable5_050514-150803173934.log >> -------------------------------------------------------------- >> preproc-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_050514 -nolog >> -------------------------------------------------------------- >> preproc-sess logfile is /dev/null >> -------------------------------------------------------------- >> $Id: preproc-sess,v 1.45.2.3 2013/01/22 22:09:10 greve Exp $ >> arodthom >> setenv FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 >> setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun >> Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC >> 2014 x86_64 x86_64 x86_64 GNU/Linux >> /autofs/cluster/roffman/users/Stable5_PerRun >> /usr/local/freesurfer/stable5_3_0/fsfast/bin/preproc-sess >> -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun -a >> SIRP_LoadRegression_Stable5_050514 -nolog >> Mon Aug 3 17:39:35 EDT 2015 >> instem f >> mc 1 f fmcpr >> stc 0 fmcpr >> sm 0 fmcpr >> mask 1 brain >> GDDA098 Template ----------------------------- >> mktemplate-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -fsd bold -rlf runlistfile -nolog -update >> >> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> ---------------- >> Mon Aug 3 17:39:36 EDT 2015 >> Detected input format at nii >> GDDA098 Update not needed >> Run: 015 ---------------- >> Mon Aug 3 17:39:36 EDT 2015 >> GDDA098 015 Update not needed >> Run: 016 ---------------- >> Mon Aug 3 17:39:36 EDT 2015 >> GDDA098 016 Update not needed >> Run: 017 ---------------- >> Mon Aug 3 17:39:36 EDT 2015 >> GDDA098 017 Update not needed >> Mon Aug 3 17:39:36 EDT 2015 >> mktemplate-sess completed >> GDDA098 Mask ------------------------ >> mkbrainmask-sess -maskstem brain -fsd bold -s GDDA098 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -rlf runlistfile -nolog -update >> ------------------------------------------------ >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> Mon Aug 3 17:39:36 EDT 2015 >> WARNING: multiple formats found for template >> USING: template.nii.gz >> GDDA098 Update not needed for session-level mask >> WARNING: multiple formats found for 015/template >> USING: 015/template.nii.gz >> GDDA098 Update not needed for run 015 mask >> GDDA098 Update not needed for run 015 meanval >> WARNING: multiple formats found for 016/template >> USING: 016/template.nii.gz >> GDDA098 Update not needed for run 016 mask >> GDDA098 Update not needed for run 016 meanval >> WARNING: multiple formats found for 017/template >> USING: 017/template.nii.gz >> GDDA098 Update not needed for run 017 mask >> GDDA098 Update not needed for run 017 meanval >> Mon Aug 3 17:39:37 EDT 2015 >> mkbrainmask-sess done >> GDDA098 Registration ----------------------------- >> register-sess -s GDDA098 -d /autofs/cluster/roffman/users/Stable5_PerRun >> -fsd bold -dof 6 -rlf runlistfile -per-run -nolog -update >> -------------------------------------------------------------- >> register-sess logfile is /dev/null >> -------------------------------------------------------------- >> Mon Aug 3 17:39:37 EDT 2015 >> >> setenv SUBJECTS_DIR /cluster/roffman/users/Stable5_PerRun >> cd /autofs/cluster/roffman/users/Stable5_PerRun >> /usr/local/freesurfer/stable5_3_0/fsfast/bin/register-sess -s GDDA098 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -dof 6 -rlf >> runlistfile -per-run -nolog -update >> >> cat: /usr/local/freesurfer/stable5_3_0/build-stamp.txt: No such file or >> directory >> Linux dauntless 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC >> 2014 x86_64 x86_64 x86_64 GNU/Linux >> >> Session: /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> ---------------- >> Mon Aug 3 17:39:37 EDT 2015 >> Run: 015 ---------------- >> Mon Aug 3 17:39:37 EDT 2015 >> WARNING: multiple formats found for bold/015/template >> USING: bold/015/template.nii.gz >> Update not needed >> Run: 016 ---------------- >> Mon Aug 3 17:39:37 EDT 2015 >> WARNING: multiple formats found for bold/016/template >> USING: bold/016/template.nii.gz >> Update not needed >> Run: 017 ---------------- >> Mon Aug 3 17:39:37 EDT 2015 >> WARNING: multiple formats found for bold/017/template >> USING: bold/017/template.nii.gz >> Update not needed >> Mon Aug 3 17:39:37 EDT 2015 >> register-sess completed >> GDDA098 MC ----------------------------- >> mc-sess -fstem f -fmcstem fmcpr -s GDDA098 -d >> /autofs/cluster/roffman/users/Stable5_PerRun -fsd bold -rlf runlistfile >> -per-run -nolog -update >> Logfile is /dev/null >> ------------------------------------------- >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> RunList: 015 016 017 >> WARNING: multiple formats found for 015/template >> USING: 015/template.nii.gz >> GDDA098 015 Update not needed >> WARNING: multiple formats found for 016/template >> USING: 016/template.nii.gz >> GDDA098 016 Update not needed >> WARNING: multiple formats found for 017/template >> USING: 017/template.nii.gz >> GDDA098 017 Update not needed >> >> >> Mon Aug 3 17:39:38 EDT 2015 >> mc-sess completed SUCCESSFULLY >> ---------------------------------------- >> Started at Mon Aug 3 17:39:35 EDT 2015 >> Ended at Mon Aug 3 17:39:38 EDT 2015 >> preproc-sess done >> ------------------------------------------- >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> Mon Aug 3 17:39:38 EDT 2015 >> anadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 >> DoGLMFit = 1 >> DoContrasts = 1 >> UpdateNeeded = 1 >> ------------------------------------------ >> ------- matlab output -------------------- >> Warning: Unable to open display 'iconic'. You will not be able to display >> graphics on the screen. >> Warning: No window system found. Java option 'MWT' ignored. >> >> < M A T L A B (R) > >> Copyright 1984-2013 The MathWorks, Inc. >> R2013b (8.2.0.701) 64-bit (glnxa64) >> August 13, 2013 >> >> No window system found. Java option 'MWT' ignored. >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com. >> >> sxa3pwd = >> >> /autofs/cluster/roffman/users/Stable5_PerRun >> >> sxa3cmd = >> >> /usr/local/freesurfer/stable5_3_0/fsfast/bin/selxavg3-sess -s GDDA098 >> -analysis SIRP_LoadRegression_Stable5_050514 >> >>>> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m >> #@# GDDA098 ############################### >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098 >> ------------------------- >> $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ >> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_selxavg3.m >> /usr/local/freesurfer/stable5_3_0/fsfast/toolbox/fast_ldanaflac.m >> /usr/local/freesurfer/stable5_3_0/matlab/MRIread.m >> ------------------------- >> outtop = /autofs/cluster/roffman/users/Stable5_PerRun >> Extension format = nii.gz >> 1 Cond2vFix.mat >> Excluding 0 points >> nruns = 3 >> autostimdur = >> >> >> outanadir = >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514 >> Excluding 0 points >> Excluding 0 points >> Excluding 0 points >> Found 49193/143360 (34.3) voxels in mask >> Creating Design Matrix >> ... creation time = 0.011 sec >> DoMCFit = 1 >> ntptot = 705, nX = 18, DOF = 687 >> Saving X matrix to >> /autofs/cluster/roffman/users/Stable5_PerRun/GDDA098/bold/SIRP_LoadRegression_Stable5_050514/Xtmp.mat >> XCond = 35.9364 (normalized) >> Computing compensation for resdual AR1 bias >> 1 -0.5 -0.507451 (t=0.033876) >> 2 -0.25 -0.264 (t=0.081305) >> 3 0 -0.0235997 (t=0.100205) >> 4 0.25 0.211292 (t=0.143646) >> 5 0.5 0.434363 (t=0.160328) >> AR1 Correction M: 0.031657 1.0595 >> Computing contrast matrices >> OLS Beta Pass >> run 1 t= 0.4 >> ERROR: dimension mismatch between mask and 1th run >>>> ------------------------------------------ >> ERROR: fast_selxavg3() failed\n >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] 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 . 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