17 Jul
2018
17 Jul
'18
4:33 a.m.
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 dgreve@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($FS_MKCON_USE_BIN == 0 && UseOctave == 0) then ...
I've put a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkcontrast2 Can you try it out?
On 07/06/2018 01:20 PM, Patrycja Naumczyk wrote:
External Email - Use CautionHi Doug,
I walked through the mkcontrast2 and found it failed when executing the loop below:
if($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.naumczyk@gmail.com mailto:patrycja.naumczyk@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 <dgreve@mgh.harvard.edu <mailto:dgreve@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 <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@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 matlabbinaries
> > 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 > <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@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.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com>> > > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@gmail.com> > <mailto:patrycja.naumczyk@gmail.com <mailto:patrycja.naumczyk@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
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> > > 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. 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