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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