New subject: Problem with FS-FAST, mkcontrast (Douglas N Greve)

1 Jul 2013


      I have matlab installed. I have the following lines in my ~/matlab/startup.m file
%------------ FreeSurfer FAST ------------------------%
fsfasthome = getenv('FSFAST_HOME');
fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
if (exist(fsfasttoolbox) == 7)
path(path,fsfasttoolbox);
end
clear fsfasthome fsfasttoolbox;
%-----------------------------------------------------%
Is there a way check to see if the path is set correctly?
Message: 9
Date: Mon, 01 Jul 2013 09:46:39 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with FS-FAST, mkcontrast
To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
Message-ID: <51D1883F.5050103@nmr.mgh.harvard.edumailto:51D1883F.5050103@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
doyou have matlab installed and in your path?
doug
On 07/01/2013 08:55 AM, O'Shea,Andrew wrote:
Hello,
I am trying to work through the FS-FAST tutorial on my data. I am
using OSX 10.6.8 with Freesurfer v. 5.1 When I get to the make
contrast command which I run
  ' mkcontrast-sess -analysis test -contrast pain-v-rest  -a 1 -c 0 '
I get the following output error:
" phhp-jcraggs-mb:Project aoshea$ mkcontrast-sess -analysis test
-contrast pain-v-rest  -a 1 -c 0
INFO: Found 1 Non-Null Conditions
INFO: Found 1 Delays
Condition Weights: 1.00000000000000000000
mkcontrast -anadir test -wcond 1.00000000000000000000 -sumconds -o
test/pain-v-rest.mat -wdelay 1 -no-octave
   $Id: mkcontrast,v 1.10 2010/07/16 16:20:10 greve Exp $
cmtxfile  test/pain-v-rest.mat
nconds    1,  wcond  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 test -wcond 1.00000000000000000000 -sumconds -o
test/pain-v-rest.mat -wdelay 1 -no-octave
Mon Jul  1 08:51:02 EDT 2013
"
It is not creating a .mat file in the analysis directory. Any
suggestions would be greatly appreciated. Thanks!
-Andrew
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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Re: [Freesurfer] Problem with FS-FAST, mkcontrast (Douglas N Greve)