External Email - Use Caution Thank you for your assistance!
I ran "export MATLAB=1", and I get a new error message: ********@***********:~/Documents/tutorial_data/fsfast-functional$ mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 INFO: Found 5 Non-Null Conditions INFO: Found 1 Delays Condition Weights: 1.00000000000000000000 0 0 0 0 mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -no-octave $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ cmtxfile my-workmem.sm05.lh/encode-v-base.mat nconds 5, wcond 1.00000000000000000000 0 0 0 0 ndelays 1, wdelay 1 ndelays 1, wpsa sumconds 1 sumdelays 0 nircorr 0 TER 0.050000 rdelta rtau cmtxfile my-workmem.sm05.lh/encode-v-base.mat monly 0 NCond 5 WCond 1.00000000000000000000 0 0 0 0 NDelay 1 WDelay 1 TER 0.050000 sumconds 1 sumdelays 0 nircorr 0 TPreStim 0 RmPreStim 0 rdelta 0 0 rtau 0 0 ndelays 1 CNorm 1 setwdelay 0 setwcond 0 Matlab file is /tmp/mkcontrast2.8414.m 1: Command not found. Tue Jul 2 16:19:34 EDT 2019 Thank you for your help! Zach ________________________________________ From: [email protected] <[email protected]> on behalf of Greve, Douglas N.,Ph.D. <[email protected]> Sent: May-30-19 7:02 PM To: [email protected] Subject: Re: [Freesurfer] "MATLAB: Undefined variable" error, FSFAST Tutorial, using Octave Try just setting MATLAB to something so that it exists, eg, set MATLAB=1 export MATLAB On 5/28/19 5:08 PM, Zacharie Saint-Georges wrote: > > External Email - Use Caution > > > Dear Freesurfer Developers, > > > I am running into a "MATLAB: Undefined variable" error while doing the > FSFAST tutorial, using Ubuntu 18.04, Freesurfer v6, and Octave***. I > did try a few solutions posted already (please see links below), but I > still cannot successfully run the tutorial command line. > > > .basrc additions for Octave environment variables > > (Ref: > https://www.mail-archive.com/[email protected]/msg21241.html): > > export FS_OCTAVE_LIB=/usr/bin/octave > export FS_OCTAVE_LIB=/usr/bin/octave > > > additional command line: > > export FS_USE_OCTAVE=1 > > Ref: > https://www.mail-archive.com/[email protected]/msg60448.html > > > main command line: > > mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 > > (tutorial page: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLevel > ) > > > > error output: > > > INFO: Found 5 Non-Null Conditions > INFO: Found 1 Delays > Condition Weights: 1.00000000000000000000 0 0 0 0 > mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir > my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o > my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile my-workmem.sm05.lh/encode-v-base.mat > nconds 5, wcond 1.00000000000000000000 0 0 0 0 > ndelays 1, wdelay 1 > ndelays 1, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > cmtxfile my-workmem.sm05.lh/encode-v-base.mat > monly 0 > NCond 5 > WCond 1.00000000000000000000 0 0 0 0 > NDelay 1 > WDelay 1 > TER 0.050000 > sumconds 1 > sumdelays 0 > nircorr 0 > TPreStim 0 > RmPreStim 0 > rdelta 0 0 > rtau 0 0 > ndelays 1 > CNorm 1 > setwdelay 0 > setwcond 0 > Matlab file is /tmp/mkcontrast2.18977.m > MATLAB: Undefined variable. > ERROR running mkcontrast > mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir > my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o > my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave > Tue May 28 16:51:41 EDT 2019 > > > I also modified the mkcontrast freesurfer file according to this post: > > Ref: > https://www.mail-archive.com/[email protected]/msg58758.html > > > > Thank you for your assistance! > > > Regards, > > Zach > > > Zacharie Saint-Georges > Research Assistant > Royal Ottawa Institute for Mental Health Research > [email protected] > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
