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
-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.