Hi Justina,
Can you send the following:
- The recon-all.log file for the subject you are trying to run through
segmentHA_T1.sh
- The output from running the `env` command
- The command you are using to invoke segmentHA_T1.sh
My guess is that the SUBJECTS_DIR environment variable isn't set correctly, but
we should also double check that recon-all completed successfully.
-Paul
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee
<justinale...@gmail.com>
Sent: Wednesday, September 14, 2022 3:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
External Email - Use Caution
Hi Paul,
This seems to have done the trick. Thank you for guiding me through this
process, I really appreciate all your help.
My last question refers to this comment when trying to run the segmentHA_T1.sh
command:
Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?
I am sure that I am referring to the right path where the files are located as
well as processing the subject with recon-all already. Is there something that
I am missing?
Thank you so much for your time.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 9:05 PM Wighton, Paul
<pwigh...@mgh.harvard.edu<mailto:pwigh...@mgh.harvard.edu>> wrote:
I think we are on the right track, but it looks like there was a space between
FREESURFER_HOME and the equal (=) sign? It also looks like there was no space
between '$FREESURFER_HOME' and './fs_install_mcr'?
The command should be copied exactly as written:
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
-Paul
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Justina Lee
<justinale...@gmail.com<mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:57 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
External Email - Use Caution
Hi Paul,
I have taken your advice and run the command as shown below:
ylee6@LAPTOP-63HA9ANS:~$ cd /usr/local/freesurfer/7.3.2/bin
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo FREESURFER_HOME
=$FREESURFER_HOME./fs_install_mcr R2019b
sudo: FREESURFER_HOME: command not found
The same problem persists yet again :( Does the problem lie somewhere else?
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul
<pwigh...@mgh.harvard.edu<mailto:pwigh...@mgh.harvard.edu>> wrote:
Ah ok, let's try this:
cd /usr/local/freesurfer/7.3.2/bin
sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
We are appending `./` to fs_install_mcr to tell it it's in the same directory.
We are also passing the definition of FREESURFER_HOME into the 'sudo'ed'
environment, because the install script relies on that.
-Paul
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Justina Lee
<justinale...@gmail.com<mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:37 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
External Email - Use Caution
Hi Paul,
I have entered the command under this directory
ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$ sudo fs_install_mcr
R2019b and the following error persists. (sudo: fs_install_mcr: command not
found)
Could there be a reason for this?
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:33 PM Wighton, Paul
<pwigh...@mgh.harvard.edu<mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
Are you in the right directory (/usr/local/freesurfer/7.3.2/bin)?
Can you try `cd /usr/local/freesurfer/7.3.2/bin` then `sudo fs_install_mcr
R2019b`?
-Paul
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Justina Lee
<justinale...@gmail.com<mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 2:28 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
External Email - Use Caution
Hi Paul,
When I try to run the installation command with sudo, the following error
command shows:
sudo: fs_install_mcr: command not found
I'm terribly sorry for the inconvenience.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 8:23 PM Wighton, Paul
<pwigh...@mgh.harvard.edu<mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
Ok so it looks like the install script is getting further and has extracted the
matlab runtime environment into a temporary directory
(/tmp/tmp.nGZQXYOgR8/install-target/v97) but during the final step, it is
trying to move that temporary directory to a location inside the FreeSurfer
directory (/usr/local/freesurfer/7.3.2/MCRv97) and it is once again running
into a 'Permission Denied' error.
Can you try re-installing the matlab runtime by running `sudo fs_install_mcr
R2019b` so that the install script has permissions to write to the FreeSurfer
directory?
-Paul
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Justina Lee
<justinale...@gmail.com<mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
External Email - Use Caution
Thank you Paul for your help!
This seems to have solved the issue, as I can now run the command
fs_install_mcr R2019b. It has ended successfully with this end message stated
below:
mv: cannot move '/tmp/tmp.nGZQXYOgR8/install-target/v97' to
'/usr/local/freesurfer/7.3.2/MCRv97': Permission denied
I think this problem persists with my next issue, which is using the command
segmentHA_T1.sh. When I try to run this command again it gives me the following
error:
ERROR: cannot find Matlab 2019b runtime in location:
/usr/local/freesurfer/7.3.2/MCRv97
It is looking for either:
bin/glnxa64/libmwlaunchermain.so (Linux 64b) or
bin/maci64/libmwlaunchermain.dylib (Mac 64b)
The hippocampal/amygdala and brainstem modules require the (free) Matlab
runtime.
You will need to download the Matlab Compiler Runtime (MCR) for Matlab 2019b.
To do so, please run the following command (you might need root permissions):
fs_install_mcr R2019b
I have seen that the pathway for fs_install_mcr is located in the
usr/local/freesurfer/7.3.2 instead of in the location stated in the error
above. When I try to search this location there is no such existing directory.
This can be the same for bin/glnxa64/libmwlaunchermain.so.
Do I need to create a new file for where the runtime should be stored? Or
create a file for the bin/glnxa64/libmwlaunchermain.so to be stored? Should the
fs_installl_mcr R2019b be stored under bin for this command to work?
Hope you can continue to help me with my follow-up issue, I appreciate it a lot.
Thank you so much.
Sincerely,
Justina
On Tue, Sep 13, 2022 at 4:35 PM Wighton, Paul
<pwigh...@mgh.harvard.edu<mailto:pwigh...@mgh.harvard.edu>> wrote:
Hi Justina,
It looks like the matlab installer is trying to use unzip but it can't find it.
Can you try running:
`sudo apt-get install unzip`
To install unzip then try the matlab installer again?
-Paul
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of You Na Lee <justinale...@gmail.com<mailto:justinale...@gmail.com>>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found
External Email - Use Caution
To whom it may concern,
Apologies for my first post, I was a little bit confounded as to how I can
reach for help.
I would like to use the segmentation of hippocampal subfields and the nuclei of
the amygdala.
Currently, I am working with Ubuntu on windows with Freesurfer 7.3.2.
I am trying to install MATLAB Runtime 2019b to run the command segmentHA_T1.sh
for the segmentation as described above. The following command shows the
corresponding error:
ylee6@LAPTOP-63HA9ANS: /usr/local/freesurfer/7.3.2/bin$ fs_install_mcr R2019b
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
100 2657M 100 2657M 0 0 10.0M 0 0:04:25 0:04:25 --:--:-- 10.1M
/usr/local/freesurfer/7.3.2/bin/fs_install_mcr: line 62: unzip: command not
found
I am currently struggling to find the solution to this issue. Is the
installation not in the correct path? Is MATLAB Runtime installed at all?
Should an already existing matlab file be deleted?
Any help would be much appreciated.
Sincerely,
Justina
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<MailScanner has detected a possible fraud attempt from "secure-web.cisco.com"
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