Hi Dusan, find out where matlab is and add it to your path. Eg, on my
mac matlab is here
/Applications/MATLAB_R2011b.app/bin/matlab
In my .cshrc file, I have
set path = ($path /Applications/MATLAB_R2011b.app/bin/matlab)
doug
On 1/26/14 9:28 AM, Dusan Hirjak wrote:
Hi Sebastian,
I typed "matlab" and "getmatlab" in my terminal, but it did not work.
When I typed getmatlab in my terminal I got the following message:
"ERROR: Cannot find matlab. Does not exist or is not in path."
Typing "matlab" is not working either:-( "command not found" is the
answer.
I guess your hypothesis is true and the matlab binary is not in my
path. Why not? What should I do next?
Thanks a lot!
DH
> Subject: Re: [Freesurfer] Freesurfer, Matlab and Maverick
> From: sebastian.moell...@rwth-aachen.de
> Date: Sun, 26 Jan 2014 10:33:33 +0100
> CC: freesurfer@nmr.mgh.harvard.edu
> To: dusanhir...@hotmail.com
>
> Hi Dusan,
>
> (I saw your PN earlier but had no idea and hence did not reply).
> But this has more information, so I try again ;)
>
>
> On Jan 25, 2014, at 02:00 , Dusan Hirjak <dusanhir...@hotmail.com>
wrote:
>
> > Dear Freesurferexperts,
> >
> > I still have the Problem because I can not run the the
mris-command to estimate the gyrification-index, because Freesurfer is
not recognizing Matlab: "ERROR: Matlab is required to run
mris_compute_lgi"
> > Im not sure why this is happening? Does someone have an idea???
>
> Could you, please open a terminal and type: 'matlab'. It should open
a matlab window, but I suspect that it does not work on your system.
My hypothesis is that either the binary/script to start matlab is not
called matlab (unlikely) or that the directory with the matlab binary
is not in your path and hence LGI can not start matlab.
> Anyway, if calling "matlab" from the terminal works my hypothesis is
falsified, but give it a try, please.
>
> best regards
> Sebastian
>
>
>
> >
> > Im starting Freesurfer as follows:
> >
> > FREESURFER_HOME=/Users/dhirjak/freesurfer
> >
> > source $FREESURFER_HOME/SetUpFreeSurfer.sh
> >
> > (than I get the following output)
> >
> > Dusan-Hirjaks-MacBook-Pro:~ dhirjak$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 --------
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME /Users/dhirjak/freesurfer
> > FSFAST_HOME /Users/dhirjak/freesurfer/fsfast
> > FSF_OUTPUT_FORMAT nii.gz
> > SUBJECTS_DIR /Users/dhirjak/MRI/Freesurfer_2
> > MNI_DIR /Users/dhirjak/freesurfer/mni
> > FSL_DIR /Users/dhirjak/fsl
> >
> > export SUBJECTS_DIR=/Users/dhirjak/MRI/Freesurfer
> >
> >
> > In have the following lines in my matlab startup-file:
> >
> > fshome = getenv('FREESURFER_HOME');
> > fsmatlab = sprintf('%s/matlab',fshome);
> > if (exist(fsmatlab) == 7)
> > path(path,fsmatlab);
> > end
> > clear fshome fsmatlab;
> > fsfasthome = getenv('FSFAST_HOME');
> > fsfasttoolbox = sprintf('%s/toolbox',fsfasthome);
> > if (exist(fsfasttoolbox) == 7)
> > path(path,fsfasttoolbox);
> > end
> > clear fsfasthome fsfasttoolbox;
> >
> > Thanks!!!
> >
> > Dusan Hirjak
> >
> >
> >
> >
> >
> >
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> >
> >
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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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