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
> 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 <dgr...@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 <dgr...@mgh.harvard.edu
> > <mailto:dgr...@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_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
> > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>
> > > <mailto:dgr...@mgh.harvard.edu <mailto:dgr...@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.naumc...@gmail.com
> > <mailto:patrycja.naumc...@gmail.com>
> > > <mailto:patrycja.naumc...@gmail.com
> > <mailto:patrycja.naumc...@gmail.com>>
> > > <mailto:patrycja.naumc...@gmail.com
> > <mailto:patrycja.naumc...@gmail.com>
> > > <mailto:patrycja.naumc...@gmail.com
> > <mailto:patrycja.naumc...@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
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > <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>>
> > >
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> > >
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