External Email - Use Caution Douglas,
thanks a lot - unfortunately this still doesn't work - it stops at the same cause: 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 Tue Jul 3 18:52:59 CEST 2018 which is apparently when verifying the $FS_MKCON_USE_BIN ? I don't have such a variable (I believe it wasn't necessary with v5.3?). Looking for it I found that a bunch of environment variables are advised in the new FS tutorial (http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup). I should probably update the .bashrc file, but I would like to clarify: 1. Are all of variables mentioned below needed for proper v6.0 FS-Fast functioning or are some of them needed only for course settings? FS_SPMREG_USE_BIN FS_MKCON_USE_BIN FS_SXA3_USE_BIN 2. To use octave instead of MATLAB - only the $FS_MKCON_USE_BIN should be set to '0', or should I change any of the other two? 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and $FS_SXA3_USE_BIN stand for? 4. Are there any other environment variables that differ between the v.5.3 and v6.0 that I should also add? Best regards, Patrycja 2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > 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. >
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