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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:
questions answered below
On 07/03/2018 01:14 PM, Patrycja Naumczyk wrote:
External Email - Use CautionDouglas,
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:
- 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
- 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).
- 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.
- 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>:
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.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>>),
> 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:Freesurfer@nmr.mgh.harvard.edu>
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