Dear Freesurfer experts,

As I run mkcontrast-sess, I receive no octave error:  

fsl@fslvm6 MT_Localizer]$ mkcontrast-sess -analysis MT.lh -contrast MS -a 1 -c 2
INFO: Found 2 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 1.00000000000000000000 -1.00000000000000000000
mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave
  $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $
cmtxfile  MT.lh/MS.mat
nconds    2,  wcond  1.00000000000000000000 -1.00000000000000000000
ndelays   1, wdelay 1
ndelays   1, wpsa  
sumconds  1
sumdelays 0
nircorr   0
TER       0.050000
rdelta   
rtau     
ERROR running mkcontrast
mkcontrast -anadir MT.lh -wcond 1.00000000000000000000 -1.00000000000000000000 -sumconds -o MT.lh/MS.mat -wdelay 1 -no-octave
Fri Oct 17 06:39:59 BST 2014

I have installed matlab and added path

/home/fsl/Desktop/freesurfer/matlab

/home/fsl/Desktop/freesurfer/fsfast/toolbox

I will appreciate in advance if you possibly could help me to solve the problem.

Best Regards,

Elahe'

Windows 7 and vmware10

Linux version:

------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 --------

Setting up environment for FreeSurfer/FS-FAST (and FSL)

FREESURFER_HOME   /home/fsl/Desktop/freesurfer

FSFAST_HOME       /home/fsl/Desktop/freesurfer/fsfast

FSF_OUTPUT_FORMAT nii.gz

SUBJECTS_DIR      /home/fsl/Desktop/freesurfer/subjects

MNI_DIR           /home/fsl/Desktop/freesurfer/mni

FSL_DIR           /usr/local/fsl

Current working directory:

pwd

/home/fsl

which freesurfer

/home/fsl/Desktop/freesurfer/bin/freesurfer

which mkanalysis-sess

/home/fsl/Desktop/freesurfer/fsfast/bin/mkanalysis-sess

which mkcontrast-sess

/home/fsl/Desktop/freesurfer/fsfast/bin/mkcontrast-sess

Command lines:

mkdir FIVA

cd FIVA

mkdir MT_Localizer

cd MT_Localizer

mkdir subj1sess1

cd subj1sess1

unpacksdcmdir -src /home/fsl/Desktop/MTLocalizer/IMAGES -targ . -run 2 bold nii f.nii -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii f.nii -run 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 bold nii f.nii -run 10 bold nii f.nii -run 11 bold nii f.nii

Within subj1sess1, made a text file named subjectname, and wrote subj001 (the name of my anatomical subject).

cd ..

preproc-sess -s subj1sess1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run

For each run, a paradigm file (paradigm.par) is included.

mkanalysis-sess -a MT.lh -surface self lh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg

mkanalysis-sess -a MT.rh -surface self rh -fsd bold -fwhm 5 -event-related -paradigm paradigm.par -nconditions 2 -refeventdur 16 -TR 2 -nskip 4 -polyfit 2 -spmhrf 0 -mcextreg

mkcontrast-sess -analysis MT.lh -contrast M_S -a 2 -c 1