External Email - Use Caution Hi Doug,
I've tried the new version You posted - it works fine as well. Many thanks! Best regards, Patrycja 2018-07-16 19:58 GMT+02:00 Douglas N. Greve <dgr...@mgh.harvard.edu>: > > 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>>> . 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 > > <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>> > > > > > > _______________________________________________ > > > 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>> > > > 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> > > > 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> > > 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 > > 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 >
_______________________________________________ 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.
