> Subject: Re: [Freesurfer] Freesurfer, Matlab and
Maverick
> From:
sebastian.moeller1@rwth-aachen.de
> Date: Sun, 26 Jan 2014 10:33:33 +0100
> CC:
freesurfer@nmr.mgh.harvard.edu
> To:
dusanhirjak@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
<dusanhirjak@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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