Sorry for the delay. I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 copy it to $FREESURFER_HOME/fsfast/bin
On 07/03/2018 12:13 PM, Patrycja Naumczyk wrote: > > > Hi all, > > I'll repost - does FSv6 no longer support octave for FS-Fast processing? > > Would appreciate clarification on this :) > Patrycja > > 2018-06-29 21:41 GMT+02:00 Patrycja Naumczyk > <patrycja.naumc...@gmail.com <mailto:patrycja.naumc...@gmail.com>>: > > Hi all, > > I just switched from FS 5.3 to 6.0 on Gentoo Linux. Previously > Freesurfer worked fine under octave setup (as specified here: > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html > > <https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-January/022135.html>), > but after the update, when I tried testing a MATLAB related > function I get an error: > > mkcontrast-sess -analysis PASAT.sm5.lh -contrast test -a 1 -c 0 > INFO: Found 2 Non-Null Conditions > INFO: Found 3 Delays > Condition Weights: 1.00000000000000000000 0 > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $ > cmtxfile PASAT.sm5.lh/test.mat > nconds 2, wcond 1.00000000000000000000 0 > ndelays 3, wdelay 1 0 0 > ndelays 3, wpsa > sumconds 1 > sumdelays 0 > nircorr 0 > TER 0.050000 > rdelta > rtau > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > mkcontrast2 -config PASAT.sm5.lh/test.config -anadir PASAT.sm5.lh > -wcond 1.00000000000000000000 0 -sumconds -o PASAT.sm5.lh/test.mat > -wdelay 1 0 0 -octave > Fri Jun 29 21:21:16 CEST 2018 > > It seems that the environment variable (FS_USE_OCTAVE) is > recognized correctly (the function runs with "-octave" flag), but > somehow is omitted during execution? What can I do about it? > > I checked that v.5.3 used mkcontrast, whereas v.6.0 uses > mkcontrast2 which does not seem to support octave? Is it possible > to force calling mkcontrast instead of mkcontrast2? > > Best regards, > Patrycja > > > > > _______________________________________________ > 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.
