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 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). 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 <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
> >
> >
> >
> >
> > _______________________________________________
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