Oh, I see now. It never failed for me because matlab is defined in my path. I think the right logic is if($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then ...
I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 Can you try it out? On 07/06/2018 01:20 PM, Patrycja Naumczyk wrote: > > External Email - Use Caution > > Hi Doug, > > I walked through the mkcontrast2 and found it failed when executing > the loop below: > > if($FS_MKCON_USE_BIN == 0) then > set MATLAB = `getmatlab`; > if($status) then > echo "ERROR: cannot find matlab. Is it in your path?" > exit 1; > endif > endif > > I changed the clause to > if($FS_MKCON_USE_BIN == 1) > as to me it didn't make sense to verify if you can find matlab in the > path, when the $FS_MKCON_USE_BIN is set to 0. Now it works OK, and > creates the contrast files as it should via octave. > > Best regards, > Patrycja > > > 2018-07-03 21:48 GMT+02:00 Patrycja Naumczyk > <patrycja.naumc...@gmail.com <mailto:patrycja.naumc...@gmail.com>>: > > OK - I double checked, and even compared the new mkcontrast2 with > the old one to verify that I copied all as I should (see below). > Still the mkcontrast2 exits when checking $FS_MKCON_USE_BIN with > the same error message (no matter if this variable is undefined or > is it defined and set to zero): > > ERROR: cannot find matlab. Is it in your path? > ERROR running mkcontrast > > 'diff' output (new > old): > > 57,163c157 > < if($UseOctave == 0) then > < echo "------- matlab output --------------------" > < cat $mfile | $MATLAB -nosplash -display iconic -nodesktop > < else > < echo "------- octave output --------------------" > < cat $mfile | octave > < endif > --- > > cat $mfile | $MATLAB -nosplash -display iconic -nodesktop > 447a442,466 > > if($UseOctave) then > > if($?FS_OCTAVE_LIB == 0) then > > echo "ERROR: you must set the FS_OCTAVE_LIB environment > variable" > > exit 1; > > endif > > if(! -e $FS_OCTAVE_LIB) then > > echo "ERROR: cannot find $FS_OCTAVE_LIB" > > exit 1; > > endif > > if($?FS_OCTAVE_BIN == 0) then > > echo "ERROR: you must set the FS_OCTAVE_BIN environment > variable" > > exit 1; > > endif > > if(! -x $FS_OCTAVE_BIN) then > > echo "ERROR: cannot find or execute $FS_OCTAVE_BIN" > > exit 1; > > endif > > if($?LD_LIBRARY_PATH == 0) setenv LD_LIBRARY_PATH "" > > if($#LD_LIBRARY_PATH == 0) then > > setenv LD_LIBRARY_PATH $FS_OCTAVE_LIB > > else > > setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:$FS_OCTAVE_LIB > > endif > > endif > > > 470a490 > > > > Probably I am omitting something, but I have no clue what is the > problem here :/ > > Patrycja > > 2018-07-03 19:35 GMT+02:00 Douglas N. Greve > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>: > > Are you sure you're using the new one? I've tested it on my > system, and > it works. > > On 07/03/2018 01:33 PM, Patrycja Naumczyk wrote: > > > > 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 <mailto:dgr...@mgh.harvard.edu> > > <mailto:dgr...@mgh.harvard.edu > <mailto: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 > <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup> > > > <http://freesurfer.net/fswiki/FsTutorial/CourseLaptopSetup > <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> > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> > > > <mailto:dgr...@mgh.harvard.edu > <mailto:dgr...@mgh.harvard.edu> <mailto: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> > > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2>> > > > > > > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 > <https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2> > > > <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>> > > > <mailto:patrycja.naumc...@gmail.com > <mailto:patrycja.naumc...@gmail.com> > > <mailto:patrycja.naumc...@gmail.com > <mailto:patrycja.naumc...@gmail.com>>> > > > <mailto:patrycja.naumc...@gmail.com > <mailto:patrycja.naumc...@gmail.com> > > <mailto:patrycja.naumc...@gmail.com > <mailto:patrycja.naumc...@gmail.com>> > > > <mailto: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>> > > > > > > > <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>>> > > > > > > > > > > > <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>> > > > > > > > <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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>>> . 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