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

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?

3. If all three are needed - what do the $FS_SPMREG_USE_BIN and $FS_SXA3_USE_BIN stand for?

4. Are there any other environment variables that differ between the v.5.3 and v6.0 that I should also add?

Best regards,

Patrycja

2018-07-03 18:31 GMT+02:00 Douglas N. Greve <dgreve@mgh.harvard.edu>:

Sorry for the delay. I've put a new version here
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>>:
>
> 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>),

> 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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