Hi Daniel, can you send me the analysis.info and Xtmp.mat files? doug Daniel Cole wrote: > > Hello Freesurfers, > > I think my last email failed to send so here it is again - > > > I'm running into problems using fs-fast for a polar only, retinotopic > analysis. > > > The error message I get is: > > > ********************* > > > Retinotopy dcole$ selxavg3-sess -analysis rtopy.self.lh -sf sessid > > Surface data self lh > > -------------------------------------------------------------- > > selxavg3-sess logfile is > /rcbiUsers/dcole/Retinotopy/log/selxavg3-sess-bold-rtopy.self.lh-120209144554.log > > -------------------------------------------------------------- > > preproc-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh > -nolog > > -------------------------------------------------------------- > > preproc-sess logfile is /dev/null > > -------------------------------------------------------------- > > $Id: preproc-sess,v 1.45.2.1 2011/03/22 17:16:19 greve Exp $ > > dcole > > setenv FREESURFER_HOME /Volumes/RCBI/freesurfer > > setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test > > Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug > 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64 > > /rcbiUsers/dcole/Retinotopy > > /Volumes/RCBI/freesurfer/fsfast/bin/preproc-sess > > -s SUB01 -d /rcbiUsers/dcole/Retinotopy -a rtopy.self.lh -nolog > > Thu Feb 9 14:45:54 EST 2012 > > instem f > > mc 1 f fmcpr > > stc 0 fmcpr > > sm 0 > > mask 1 brain > > SUB01 Template ----------------------------- > > mktemplate-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold > -nolog -update > > > > Session: /rcbiUsers/dcole/Retinotopy/SUB01 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > Detected input format at nii > > SUB01 Update not needed > > Run: 001 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > SUB01 001 Update not needed > > Run: 002 ---------------- > > Thu Feb 9 14:45:54 EST 2012 > > SUB01 002 Update not needed > > Run: 003 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 003 Update not needed > > Run: 004 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 004 Update not needed > > Run: 005 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 005 Update not needed > > Thu Feb 9 14:45:55 EST 2012 > > mktemplate-sess completed > > SUB01 Mask ------------------------ > > mkbrainmask-sess -maskstem brain -fsd bold -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -nolog -update > > ------------------------------------------------ > > /rcbiUsers/dcole/Retinotopy/SUB01 > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 Update not needed for session-level mask > > SUB01 Update not needed for run 001 mask > > SUB01 Update not needed for run 001 meanval > > SUB01 Update not needed for run 002 mask > > SUB01 Update not needed for run 002 meanval > > SUB01 Update not needed for run 003 mask > > SUB01 Update not needed for run 003 meanval > > SUB01 Update not needed for run 004 mask > > SUB01 Update not needed for run 004 meanval > > SUB01 Update not needed for run 005 mask > > SUB01 Update not needed for run 005 meanval > > Thu Feb 9 14:45:55 EST 2012 > > mkbrainmask-sess done > > SUB01 Registration ----------------------------- > > register-sess -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 > -per-run -nolog -update > > -------------------------------------------------------------- > > register-sess logfile is /dev/null > > -------------------------------------------------------------- > > Thu Feb 9 14:45:55 EST 2012 > > > setenv SUBJECTS_DIR /Volumes/rcbiUsers/dcole/Retinotopy/Subjects/test > > cd /rcbiUsers/dcole/Retinotopy > > /Volumes/RCBI/freesurfer/fsfast/bin/register-sess -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -fsd bold -dof 6 -per-run -nolog -update > > > freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 > > Darwin commissure.local 11.2.0 Darwin Kernel Version 11.2.0: Tue Aug > 9 20:54:00 PDT 2011; root:xnu-1699.24.8~1/RELEASE_X86_64 x86_64 > > > > Session: /rcbiUsers/dcole/Retinotopy/SUB01 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Run: 001 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 002 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 003 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 004 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Run: 005 ---------------- > > Thu Feb 9 14:45:55 EST 2012 > > Update not needed > > Thu Feb 9 14:45:55 EST 2012 > > register-sess completed > > SUB01 MC ----------------------------- > > mc-sess -fstem f -fmcstem fmcpr -s SUB01 -d > /rcbiUsers/dcole/Retinotopy -fsd bold -per-run -nolog -update > > Logfile is /dev/null > > ------------------------------------------- > > /rcbiUsers/dcole/Retinotopy/SUB01 > > RunList: 001 002 003 004 005 > > SUB01 001 Update not needed > > SUB01 002 Update not needed > > SUB01 003 Update not needed > > SUB01 004 Update not needed > > SUB01 005 Update not needed > > > > Thu Feb 9 14:45:55 EST 2012 > > mc-sess completed SUCCESSFULLY > > SUB01 To Surface ----------------------------- > > rawfunc2surf-sess -fwhm 5 -s SUB01 -d /rcbiUsers/dcole/Retinotopy -fsd > bold -hemi lh -self -nolog -update > > instem fmcpr > > outstem fmcpr.sm5.self.hemi > > ------------------------------ > > 1/1 SUB01 > > 1/1 SUB01 001 lh --------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 001 Update not needed > > 1/1 SUB01 002 lh --------- > > Thu Feb 9 14:45:55 EST 2012 > > SUB01 002 Update not needed > > 1/1 SUB01 003 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > SUB01 003 Update not needed > > 1/1 SUB01 004 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > SUB01 004 Update not needed > > 1/1 SUB01 005 lh --------- > > Thu Feb 9 14:45:56 EST 2012 > > SUB01 005 Update not needed > > > Thu Feb 9 14:45:56 EST 2012 > > rawfunc2surf-sess completed > > ---------------------------------------- > > Started at Thu Feb 9 14:45:54 EST 2012 > > Ended at Thu Feb 9 14:45:56 EST 2012 > > preproc-sess done > > ------------------------------------------- > > /rcbiUsers/dcole/Retinotopy/SUB01 > > Thu Feb 9 14:45:56 EST 2012 > > anadir = /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh > > 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. > > 2012-02-09 14:45:56.773 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.775 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.776 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.777 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.778 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.779 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.780 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.781 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.783 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.796 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.797 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.798 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.812 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.813 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:56.815 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > > < M A T L A B (R) > > > Copyright 1984-2010 The MathWorks, Inc. > > Version 7.10.0.499 (R2010a) 64-bit (maci64) > > February 5, 2010 > > > 2012-02-09 14:45:57.634 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.636 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.637 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.638 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.639 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.640 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.641 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.642 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.643 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.644 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.645 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.646 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.647 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.648 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.649 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.650 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.651 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.652 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.653 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.654 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.655 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.656 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.657 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.658 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.659 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.660 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.661 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.662 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.663 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.664 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.665 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.666 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.667 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.668 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.669 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > 2012-02-09 14:45:57.670 MATLAB[17738:7103] This process is attempting > to exclude an item from Time Machine by path without administrator > privileges. This is not supported. > > > > To get started, type one of these: helpwin, helpdesk, or demo. > > For product information, visit www.mathworks.com > <http://www.mathworks.com/>. > > > > >> >> >> >> >> >> >> > /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m > > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > > #@# SUB01 ############################### > > /rcbiUsers/dcole/Retinotopy/SUB01 > > ------------------------- > > $Id: fast_selxavg3.m,v 1.100 2011/03/02 16:14:38 greve Exp $ > > /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_selxavg3.m > > /Volumes/RCBI/freesurfer/fsfast/toolbox/fast_ldanaflac.m > > /Volumes/RCBI/freesurfer/matlab/MRIread.m > > ------------------------- > > outtop = /rcbiUsers/dcole/Retinotopy > > Extension format = nii.gz > > nruns = 5 > > autostimdur = > > > > outanadir = /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh > > Found 15746/149363 <tel:15746%2F149363> (10.5) voxels in mask > > Creating Design Matrix > > ... creation time = 0.011 sec > > DoMCFit = 1 > > ntptot = 1305, nX = 39, DOF = 1266 > > Saving X matrix to > /rcbiUsers/dcole/Retinotopy/SUB01/bold/rtopy.self.lh/Xtmp.mat > > ??? Error using ==> svd > > Input to SVD must not contain NaN or Inf. > > > Error in ==> cond at 40 > > s = svd(A); > > > Error in ==> fast_selxavg3 at 254 > > XCond = cond(XtX); > > > > >> ------------------------------------------ > > ERROR: fast_selxavg3() failed\n > > > ********************* > > > I think the problem is with the "??? Error using ==> svd... " error, > not the matlab errors. I've found that many people were reporting > this matlab error but it's presumably more of an annoyance than a > technical issue. > > > I'm following the tutorial > at > http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis > . I'm pretty sure I have my directories set up properly and I've used > Mricron's dcm2nii tool on my raw functionals/structurals. I've also > already successfully preprocessed my data and made the rtopy.par files > (preproc-sess & mkanalysis-sess). > > I haven't been able to find a response that fixed the problem and was > hoping for some suggestions. > > > Thanks so much, > > Daniel > > > -- > > Daniel Cole > > University of Rochester > > Brain and Cognitive Sciences > > dcol...@u.rochester.edu <mailto:dcol...@u.rochester.edu> > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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: 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.
