Thanks Bruce.

On Fri, Sep 16, 2016 at 2:02 PM, Bruce Fischl <fis...@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
>>
>> --
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>> Alan N. Francis PhD
>> Instructor - Imaging Neuroscience
>> Brain Imaging Center
>> McLean Hospital
>> Harvard Medical School
>> 115 Mill Street, Belmont, MA 02478
>> al...@bwh.harvard.edu
>> afran...@mclean.harvard.edu
>>
>>
>>
>> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
>>
>>
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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
al...@bwh.harvard.edu <ezra_wegbr...@brown.edu>
afran...@mclean.harvard.edu


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