External Email - Use Caution Douglas,
thank you for clarifying. The problem is that both when $FS_MKCON_USE_BIN is not defined and when it is set to '0' mkcontrast2 asks for MATLAB path (as in my previous mail). What should I do to make it use octave instead? Best regards, Patrycja 2018-07-03 19:23 GMT+02:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > questions answered below > > On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote: > > > > 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 > These are only needed if you want to use the matlab binaries > > 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? > Just FS_MKCON_USE_BIN(or leave it undefined). > > 3. If all three are needed - what do the $FS_SPMREG_USE_BIN and > > $FS_SXA3_USE_BIN stand for? > These are to use the matlab binaries when running these programs > (binaries don't require a license). We do not use spm for registration > anymore, so that this irrelevant. SXA3 refers to selxavg3-sess. > > 4. Are there any other environment variables that differ between the > > v.5.3 and v6.0 that I should also add? > I don't think so. > > > > Best regards, > > Patrycja > > > > > > > > 2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgr...@mgh.harvard.edu > > <mailto:dgr...@mgh.harvard.edu>>: > > > > Sorry for the delay. I've put a new version here > > https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 > > <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> > > <mailto: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> > > > > > <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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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. > > > > > > > > > > _______________________________________________ > > 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 >
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