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/SetUpFreeSurfer.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
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
_______________________________________________
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.
