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), 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