Thanks Bruce.

On Fri, Sep 16, 2016 at 2:02 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Alan

make sure matlab is in your path. You can check by typing:

which matlab

cheers Bruce

On Fri, 16 Sep 2016, Alan Francis wrote:

Hi Marie -

...

I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I am unable to get FreeSurfer to recognize this (see below) , so I am getting an error. Is there any way to overcome this?

Thanks,

Alan

afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer afrancis-mac:~ afrancis$ source /Applications/freesurfer/SetUp FreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl afrancis-mac:~ afrancis$ export MATLABPATH=/Applications/MATLAB_R2015a.app/bin afrancis-mac:~ afrancis$ export PATH=${MATLABPATH}/bin:${PATH} afrancis-mac:~ afrancis$ recon-all -s DM55 -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 root wheel 948660 Sep 16 09:50 /Applications/freesurfer/subjects/DM55/scripts/recon-all.log Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Applications/freesurfer/subjects/DM55/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Sep 16 09:55:23 EDT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64

recon-all -s DM55 exited with ERRORS at Fri Sep 16 09:55:23 EDT 2016

For more details, see the log file /Applications/freesurfer/subjects/DM55/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Alan N. Francis PhD Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu afrancis@mclean.harvard.edu

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