Hi Wei,
Did you run these commands with sudo?
Cheers,
/E
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.org>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, October 1, 2020 at 14:58
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Matlab Matlab Runtime issue
External Email - Use Caution
Hello, Freesurfer team
My name is Wei Shao, FS user, I have a few questions regarding the Matlab package and the hippocampal subfield function with FS.
I have followed the instruction from the website to install Matlab, sue the fs_install_mcr R2014b
(Oct 01, 2020 14:41:05) Exiting with status 0
(Oct 01, 2020 14:41:05) End - Successful.
Finished
MCR v84 (R2014b) already exists in /usr/local/freesurfer/7.1.0-1
do you want to reinstall? [y/n]
exiting without install
However, when I try to use the hippocampal seg command:
segmentHA_T1.sh, it gives me this error
ERROR: cannot find Matlab 2014b runtime in location:
/usr/local/freesurfer/7.1.0-1/MCRv84
The hippocampal/amygdala and brainstem modules require the (free) Matlab runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2014b.
To do so, please run the following commands (you might need root permissions):
LINUX:
cd /usr/local/freesurfer/7.1.0-1
curl "https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=runtime2014bLinux.tar.gz" -o "runtime2014b.tar.gz"
tar xvf runtime2014b.tar.gz
Even after I did this as the following, it still gave me the same response when I tried segmentHA_T1.sh.
Could you tell me how to fix this? Thanks!
Best,
Wei