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 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.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 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>
> <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
> <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>>>
> > > >
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> >
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> >
>   <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>>>
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