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&am..." -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
Hi Wei, Did you run these commands with sudo? Cheers, /E
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
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&am..." -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
External Email - Use Caution
HI, There
sorry for the late reply, I didn't see the reply due to the email setting issues. I have tried the sudo command, but it still gave me the same error.
Best, Wei
On Thu, Oct 1, 2020 at 2:56 PM Wei Shao wshao@research.baycrest.org wrote:
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&am..." -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
Uuuummm about you try deleting the MCR from /usr/local/freesurfer/7.1.0-1 before reinstalling? Cheers, /Eugenio
Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com
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: Wednesday, October 7, 2020 at 23:21 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Matlab Matlab Runtime issue
External Email - Use Caution HI, There
sorry for the late reply, I didn't see the reply due to the email setting issues. I have tried the sudo command, but it still gave me the same error.
Best, Wei
On Thu, Oct 1, 2020 at 2:56 PM Wei Shao <wshao@research.baycrest.orgmailto:wshao@research.baycrest.org> wrote: 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&am..." -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
freesurfer@nmr.mgh.harvard.edu
-
Iglesias Gonzalez, Juan E. -
Wei Shao