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Dear Freesurfer Developers,

I am running into a "MATLAB: Undefined variable" error while doing the FSFAST tutorial, using Ubuntu 18.04, Freesurfer v6, and Octave***. I did try a few solutions posted already (please see links below), but I still cannot successfully run the tutorial command line.

.basrc additions for Octave environment variables

(Ref:  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg21241.html):

additional command line:

export FS_USE_OCTAVE=1

Ref:  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg60448.html

main command line:

mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1

(tutorial page:  https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastFirstLevel )

error output:

INFO: Found 5 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 1.00000000000000000000 0 0 0 0
mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave
  $Id: mkcontrast2,v 1.3 2016/03/11 23:46:48 greve Exp $
cmtxfile  my-workmem.sm05.lh/encode-v-base.mat
nconds    5,  wcond  1.00000000000000000000 0 0 0 0
ndelays   1, wdelay 1
ndelays   1, wpsa   
sumconds  1
sumdelays 0
nircorr   0
TER       0.050000
rdelta    
rtau      
  cmtxfile  my-workmem.sm05.lh/encode-v-base.mat
  monly  0
  NCond   5
  WCond   1.00000000000000000000 0 0 0 0
  NDelay  1
  WDelay  1
  TER         0.050000
  sumconds   1
  sumdelays  0
  nircorr  0
  TPreStim  0
  RmPreStim  0
  rdelta     0 0
  rtau       0 0
  ndelays    1
  CNorm      1
  setwdelay  0
  setwcond   0
Matlab file is /tmp/mkcontrast2.18977.m
MATLAB: Undefined variable.
ERROR running mkcontrast
mkcontrast2 -config my-workmem.sm05.lh/encode-v-base.config -anadir my-workmem.sm05.lh -wcond 1.00000000000000000000 0 0 0 0 -sumconds -o my-workmem.sm05.lh/encode-v-base.mat -wdelay 1 -octave
Tue May 28 16:51:41 EDT 2019

I also modified the mkcontrast freesurfer file according to this post:

Ref:  https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58758.html

Thank you for your assistance!

Regards,

Zach