3 Jul
2018
3 Jul
'18
3:48 p.m.
External Email - Use Caution
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 endifendif
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:
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 CautionDouglas,
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>:
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>). 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_BINshould
> 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 betweenthe
> 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>>>: > > 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>> > 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>>>>: > > > > 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>>>),
> > 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>> > > 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>> > > > 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>> . 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> > 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>
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