Dear all,
I am trying to repeat FS-Fast tutorial on my data. The system that I use is a
Neurodebian running through a virtual machine CentOS 4 x86_64 and freesurfer
version is v5.3.0 The error that I get during mkcontrast is as below:
mkcontrast-sess log file
$Id: mkcontrast-sess,v 1.17 2011/03/15 16:50:48 greve Exp $
$0
Linux neurodebian 3.2.0-4-amd64 #1 SMP Debian 3.2.65-1+deb7u1 x86_64 GNU/Linux
Tue Apr 21 06:44:13 EDT 2015
-analysis Analysis_PreprocFsTest -contrast FvsO -a 2 -c 1
/usr/local/freesurfer/fsfast/bin/mkcontrast
Condition Weights: -1.00000000000000000000 1.00000000000000000000
mkcontrast -anadir Analysis_PreprocFsTest -wcond -1.00000000000000000000
1.00000000000000000000 -sumconds -o Analysis_PreprocFsTest/FvsO.mat -wdelay 1
-no-octave
$Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
cmtxfile Analysis_PreprocFsTest/FvsO.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: cannot find matlab. Is it in your path?
ERROR running mkcontrast
mkcontrast -anadir Analysis_PreprocFsTest -wcond -1.00000000000000000000
1.00000000000000000000 -sumconds -o Analysis_PreprocFsTest/FvsO.mat -wdelay 1
-no-octave
Tue Apr 21 06:18:45 EDT 2015
Matlab is actually in the path. I can call it from the pwd. Fsfast toolbox has
been added to matlab path and startup.m file is:
%------------ FreeSurfer -----------------------------%
fshome = getenv('FREESURFER_HOME');
fsmatlab = sprintf('%s/matlab',fshome);
if (exist(fsmatlab) == 7)
path(path,fsmatlab);
end
clear fshome fsmatlab;
%-----------------------------------------------------%
%------------ FreeSurfer FAST ------------------------%
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-----------------------------------------------------%
I tried to make a link: sudo ln -s /usr/local/MATLAB/R2012b/bin/matlab to
/usr/local/freesurfer/fsfast/bin. In this case, it generates the contrast mat
file but shows a warning:
hoffmann@neurodebian:/mnt/host/PreprocFsTest$ mkcontrast-sess -analysis
Analysis_PreprocFsTest -contrast FvsO -a 2 -c 1
INFO: Found 2 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: -1.00000000000000000000 1.00000000000000000000
mkcontrast -anadir Analysis_PreprocFsTest -wcond -1.00000000000000000000
1.00000000000000000000 -sumconds -o Analysis_PreprocFsTest/FvsO.mat -wdelay 1
-no-octave
$Id: mkcontrast,v 1.10.2.1 2011/09/27 15:56:27 greve Exp $
cmtxfile Analysis_PreprocFsTest/FvsO.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
Warning: Unable to open display 'iconic'. You will not be able to display
graphics on the screen.
Warning: No window system found. Java option 'MWT' ignored.
< M A T L A B (R) >
Copyright 1984-2012 The MathWorks, Inc.
R2012b (8.0.0.783) 64-bit (glnxa64)
August 22, 2012
No window system found. Java option 'MWT' ignored.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com<http://www.mathworks.com>.
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
>> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> Normalizing contrast matrix
>> >> >> >> >> >> >> >> Tue Apr 21 06:44:16 EDT 2015
Is this related to the further errors that I receive while doing selxavg3-sess
in: ==> fmri_hemodyn
> > Too many input argument.?
Any help is greatly appreciated.
Best regards,
Khazar Ahmadi
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