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.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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