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 <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>>:
>
>     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
>     <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
>     >     >
>     >     >
>     >     >
>     >     >
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