Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

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 
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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* 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   TimeTime Time
> Current
>
>  Dload  Upload   Total   SpentLeft
> Speed
>
> 100 2657M  100 2657M0 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
>
>
>
>
>
>
>
> Sent from Mail
> 
> for Windows
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/13hztnzjV4NG8MRS_WPAvkQDaoH3MtDTzQGVDegG1V9tB3vNAeQxThejPX_wGtCRjJ3QWFM_JqnS5VBaOktcLzveKxjIX3MA5p2FjSdBZCoFXLtQ8Z1KyKvtTr-aGSjUmS03KRcPg02rCBvEhWmoJbDCQsf8zWfExuxR-u4fl-PYnkCrPWM9hUnmXrZd2WEFL8AmEvxNDuEdQuaMSEDPGPtvx0RN5AfCTFUb79CJ6vuveAr1iWf0-gU3NHQNZ1vKIkflLgYP8q2yBFTSLhEcUy23TWxVYYoANhKGSeUYuR2Lsdk56Uy1D8vvtTbV9Gc1XKCXLh1Ig_3pL6k_OJiakhw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> The information in this e-mail is intended only for the person to whom it
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> e-mail contains patient information, please contact the Mass General
> Brigham Compliance HelpLine at
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Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

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 
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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list 
> *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 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* 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   TimeTime Time
> Current
>
>  Dload  Upload   Total   SpentLeft
> Speed
>
> 100 2657M  100 2657M0 0  10.0M  0  0

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

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 
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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list 
> *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 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list 
> *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 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of You Na Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 9:01 AM
> *To:* freesurfe

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

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 
wrote:

> Ah ok, let's try this:
>
> cd /usr/local/freesurfer/7.3.2/bin
> sudo FREESURFER_HOME=$FREESURFER_HOME ./fs_install_mcr R2019b
>
> We are appending `./` to fs_install_mcr to tell it it's in the same
> directory.  We are also passing the definition of FREESURFER_HOME into the
> 'sudo'ed' environment, because the install script relies on that.
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:37 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> I have entered the command under this directory 
> ylee6@LAPTOP-63HA9ANS:/usr/local/freesurfer/7.3.2/bin$
> 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 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list 
> *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 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 1:58 PM
> *To:* Freesurfer support list 
> *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_inst

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

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 
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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:57 PM
> *To:* Freesurfer support list 
> *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 =$FREESURFER_HOME./fs_install_mcr R2019b
> sudo: FREESURFER_HOME: command not found
>
> The same problem persists yet again :( Does the problem lie somewhere else?
>
> Sincerely,
> Justina
>
> On Tue, Sep 13, 2022 at 8:49 PM Wighton, Paul 
> wrote:
>
> Ah ok, let's try this:
>
> cd /usr/local/freesurfer/7.3.2/bin
> sudo FREESURFER_HOME=$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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:37 PM
> *To:* Freesurfer support list 
> *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 
> 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 <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Tuesday, September 13, 2022 2:28 PM
> *To:* Freesurfer support list 
> *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 
> 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 <
> 

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

Thank you for all your help with some technical issues.
I was wondering if you could help me with one tiny issue I have been unable
to solve, which is the usage of freeview on my computer.
The installation has been completed successfully, but when I try to open
any data, I seem to not see anything. Upon trying again recently, now
opening freeview does not seem to work at all. (For example, trying to run
the command freeview -v T1.mgz does not produce a freeview to open up on
another window.)
Could you help me with this? I'm sorry for the troubles once more.

Sincerely,
Justina

On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
wrote:

> One more note:
>
> The command:
> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
>
> May or may not work, depending on the type of shell environment you are
> using.  If it doesn't work, you can try:
> setenv SUBJECTS_DIR /home/ylee6/ADIPA_data
>
> To set the environment variable
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <
> pwigh...@mgh.harvard.edu>
> *Sent:* Thursday, September 15, 2022 9:56 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
> Hi Justina,
>
> Ok so on your computer, the subjects are located in
> /home/ylee6/ADIPA_data, but the SUBJECTS_DIR environment variable is set to
> /usr/local/freesurfer/7.3.2/subjects.
>
> There are two ways we can fix this.
>
> 1) We can change the SUBJECTS_DIR environment variable and then run
> segmentHA_T1.sh:
>
> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
> segmentHA_T1.sh 26
>
> 2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh,
> telling it to use that directory instead of the environment variable:
>
> segmentHA_T1.sh 26 /home/ylee6/ADIPA_data
>
> You were close with your command "segmentHA_T1.sh 26
> [/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter
> in square brackets ([]) it means the parameter is optional, you shouldn't
> include the brackets when running the command.
>
> Glad I could be helpful,
>
> -Paul
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
> justinale...@gmail.com>
> *Sent:* Thursday, September 15, 2022 7:51 AM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not
> found
>
>
> External Email - Use Caution
>
> Hi Paul,
>
> Thank you for your help tremendously throughout this process.
>
> Firstly, attached you will find the requested recon-all.log for the
> subject 26 (originally located in the path
> /home/ylee6/ADIPA_data/26/scripts), in which at the end of the log you
> can see that the recon-all is completed successfully.
>
> Secondly, with the output from the 'env' command you can see it described
> as such below:
>
> SHELL=/bin/bash
> WSL_DISTRO_NAME=Ubuntu
> OS=Linux
> MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
> FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
> FREESURFER=/usr/local/freesurfer/7.3.2
> MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
> FS_OVERRIDE=0
> NAME=LAPTOP-63HA9ANS
> PWD=/home/ylee6/ADIPA_data/26/mri
> LOGNAME=ylee6
> FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
> MOTD_SHOWN=update-motd
> HOME=/home/ylee6
> LANG=C.UTF-8
> WSL_INTEROP=/run/WSL/8_interop
> MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
>
> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=0

Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command not found

[Justina Lee]

External Email - Use Caution

Hi Paul,

Redownloading freesurfer seems to have done the trick, but I still come
across the issue with loading data and seeing nothing on freeview. Hope you
can help me with this tiny problem.

Sincerely,
Justina

On Fri, Sep 30, 2022 at 10:10 AM Justina Lee  wrote:

> Hi Paul,
>
> Thank you for all your help with some technical issues.
> I was wondering if you could help me with one tiny issue I have been
> unable to solve, which is the usage of freeview on my computer.
> The installation has been completed successfully, but when I try to open
> any data, I seem to not see anything. Upon trying again recently, now
> opening freeview does not seem to work at all. (For example, trying to run
> the command freeview -v T1.mgz does not produce a freeview to open up on
> another window.)
> Could you help me with this? I'm sorry for the troubles once more.
>
> Sincerely,
> Justina
>
> On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul 
> wrote:
>
>> One more note:
>>
>> The command:
>> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
>>
>> May or may not work, depending on the type of shell environment you are
>> using.  If it doesn't work, you can try:
>> setenv SUBJECTS_DIR /home/ylee6/ADIPA_data
>>
>> To set the environment variable
>>
>> -Paul
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <
>> pwigh...@mgh.harvard.edu>
>> *Sent:* Thursday, September 15, 2022 9:56 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
>> not found
>>
>> Hi Justina,
>>
>> Ok so on your computer, the subjects are located in
>> /home/ylee6/ADIPA_data, but the SUBJECTS_DIR environment variable is set to
>> /usr/local/freesurfer/7.3.2/subjects.
>>
>> There are two ways we can fix this.
>>
>> 1) We can change the SUBJECTS_DIR environment variable and then run
>> segmentHA_T1.sh:
>>
>> export SUBJECTS_DIR=/home/ylee6/ADIPA_data
>> segmentHA_T1.sh 26
>>
>> 2) Or, we can pass the subjects dir as a parameter to segmentHA_T1.sh,
>> telling it to use that directory instead of the environment variable:
>>
>> segmentHA_T1.sh 26 /home/ylee6/ADIPA_data
>>
>> You were close with your command "segmentHA_T1.sh 26
>> [/usr/local/freesurfer/7.3.2/subjects]"! Just FYI when you see a parameter
>> in square brackets ([]) it means the parameter is optional, you shouldn't
>> include the brackets when running the command.
>>
>> Glad I could be helpful,
>>
>> -Paul
>> --
>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
>> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Justina Lee <
>> justinale...@gmail.com>
>> *Sent:* Thursday, September 15, 2022 7:51 AM
>> *To:* Freesurfer support list 
>> *Subject:* Re: [Freesurfer] Freesurfer: fs_install_mcr: Unzip command
>> not found
>>
>>
>> External Email - Use Caution
>>
>> Hi Paul,
>>
>> Thank you for your help tremendously throughout this process.
>>
>> Firstly, attached you will find the requested recon-all.log for the
>> subject 26 (originally located in the path
>> /home/ylee6/ADIPA_data/26/scripts), in which at the end of the log you
>> can see that the recon-all is completed successfully.
>>
>> Secondly, with the output from the 'env' command you can see it described
>> as such below:
>>
>> SHELL=/bin/bash
>> WSL_DISTRO_NAME=Ubuntu
>> OS=Linux
>> MINC_BIN_DIR=/usr/local/freesurfer/7.3.2/mni/bin
>> FSFAST_HOME=/usr/local/freesurfer/7.3.2/fsfast
>> FREESURFER=/usr/local/freesurfer/7.3.2
>> MNI_DATAPATH=/usr/local/freesurfer/7.3.2/mni/data
>> FS_OVERRIDE=0
>> NAME=LAPTOP-63HA9ANS
>> PWD=/home/ylee6/ADIPA_data/26/mri
>> LOGNAME=ylee6
>> FUNCTIONALS_DIR=/usr/local/freesurfer/7.3.2/sessions
>> MOTD_SHOWN=update-motd
>> HOME=/home/ylee6
>> LANG=C.UTF-8
>> WSL_INTEROP=/run/WSL/8_interop
>> MINC_LIB_DIR=/usr/local/freesurfer/7.3.2/mni/lib
>>
>> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;3

[Freesurfer] Freeview does not display image

[Justina Lee]

External Email - Use Caution

To whom that can provide any insight,

I am currently using Ubuntu on windows to open freeview to show some data.
My issue at hand is that freeview does not show any images, despite
changing the window levels (contrast and brightness). Using the command
freeview -v works, and I am able to run it smoothly. When I try to open an
mgz file, it runs fine, but I am unable to see anything.

 I do not have VirtualBox installed and tried to take this advice from
previous but I ran across the problem of downloading the course Virtual
Machine. I do think that I do not need to download the VirtualBox and can
continue using Ubuntu on Windows.

What could be the issue with this? Should I be downloading the Virtual
machine to run Freeview?

Thank you so much for your time and I hope that my issue is not too big of
a problem to solve.

Sincerely,
Justina
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview does not display image

[Justina Lee]

External Email - Use Caution

Hello R,

Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows
subsystem linux (WSL). I followed these instructions at
https://secure-web.cisco.com/1p8Cin-EJEpeRx1cZi8s231xYYwEa73Ljn6cCDVMGOudNzx-clBR6sZUCDMeSmSC85H7RtRtyEHdxO6j7DqYMFXEEle0HWR03qo71o_mjxHnvDmseEhe6KVuhPF3a9EM59Nka9FTcsYt1gVTr_HvvTbhHKoEmZ7oV9i3KeY7rIQGCvfTf9bQme8kx7TWvoWnm5VKZSHSvq48kfOuo2C6lIY_MAf92M9I1KgyaWazv2MhWZWGikJgOV2nw4QC69vFLjpH3ctxn4UIMJLn7bY8klGzGH6U_lmVmi2m4Q1eV11REMBdDeMc-XzcjqJYUvXvg-Th-bs5WT8twMoaIT9Yw2A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl
 to download the WSL,
X-server, and the freesurfer.

 Is it still possible to fix the problem here internally or should I follow
the instructions sent from the link previously to download Virtual Box and
run freesurfer in this way? I have been trying to open the zip file Ubuntu
compressed image but it seems to keep crashing as I load it. I will keep
trying if the first way aforementioned is not possible.

Thank you and hope this has become alittle clearer.

Sincerely,
Justina


On Mon, Oct 3, 2022 at 8:35 PM fsbuild  wrote:

> External Email - Use Caution
>
>
> Hello Justina,
>
> We need to know what your setup is on Windows for running Linux in order
> to help with running freeview.  It reads like you are not using VirtualBox
> to run the Linux Ubuntu OS,
>
>  I do not have VirtualBox installed 
>
>
> So it’s not clear to me how you are currently running Ubuntu Linux on your
> Windows machine in order to run freeview or other freesurfer commands.  Are
> you running Ubuntu linux with the Windows Subsystem for Linux (WSL)?  Maybe
> you are connecting remotely to a linux machine via VNC or the like from
> your Windows machine ?
>
> If you don’t mind running freesurfer 7..2.0 (instead of the newest 7.3.2
> release), there is a smaller version of the VM to download from *MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be* 
> https://secure-web.cisco.com/1paaB_cgPVQ7btidlPguZcJsmtliH8F8hjmenNiwMMKj6psPWB7PbCzz88mGy5PUxJ4_RYJHEnEgzOrASI38A31sVxjVmfxfUSo9L9FoxfPo2Av_MQ6ngrK-iKSLjkEbUggeuaoXemH1U78dhZuZM2A4CAL_oLkIUIFvyvWpHvLbzriR6DhJXh-EgzZuO82YSUqI3pVfRIQ1T5aFoSn8Y-hAXTf-f5_IS6TEMtEMFUpxxu98IMgpvc-KXmk-Wzm8NyBtiXkhuju9KJHm65VHaV7mHETaWMKcy3_JUxpNDLu3RFKJJlU9p2uLb6LOYUMWA_NvQjUVmIQKA27QoJS_YzA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67
> <https://secure-web.cisco.com/1nGqawfrSjzBkLop5W-SrkfQ2ibvmMoS5qotzl9aEXpoPbx8_8oZjitfcumpYwJzIif-wByimOIG0sV2h8pSCgX9w6OEOFEhgkJVHSFViAa9o6K5k7LpzYBn0K7WN1P-7Dh8TSOSMCYv3wV9ZWcWY6-I8SrPHmKs5tRLZT4R-CVmoTNgDd_naVSpFLVaVLBV8VE0fbOEyTJzRgR08Cvslb1_3U1Cz1l5k1JGUw_7lqG49yLe_HS-LpZ9PHoc_hH4vTBzHdnPsDFVFmmRZ_9MyWPJqnqMVibdj1FLfCFam6PSnzQlydbNsqCw_9NjdGDiu/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67>
> with setup instructions under that link.   But you would still need to
> download and install VirtualBox on your Windows machine and then download
> and install the Freesurfer Software.
>
> - R.
>
> On Oct 3, 2022, at 09:35, Justina Lee  wrote:
>
> External Email - Use Caution
>
>
> To whom that can provide any insight,
>
> I am currently using Ubuntu on windows to open freeview to show some data.
> My issue at hand is that freeview does not show any images, despite
> changing the window levels (contrast and brightness). Using the command
> freeview -v works, and I am able to run it smoothly. When I try to open an
> mgz file, it runs fine, but I am unable to see anything.
>
>  I do not have VirtualBox installed and tried to take this advice from
> previous but I ran across the problem of downloading the course Virtual
> Machine. I do think that I do not need to download the VirtualBox and can
> continue using Ubuntu on Windows.
>
> What could be the issue with this? Should I be downloading the Virtual
> machine to run Freeview?
>
> Thank you so much for your time and I hope that my issue is not too big of
> a problem to solve.
>
> Sincerely,
> Justina
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1XBB9mVISZMBi-_VRhIEm62UucxuNsrx0F-92EzExHgsYK_1D4N3Dg9If49qUFuo11Cdn9sLRgmZ46jVvgxo6jP2o7lsQu7bhK6-Kmis1M884MqF9f3CYVJizJM92RHyc69rt33Kug3_Ex5lc4S1Lwy1cldPGDcO_12gxyVoS4xQ-hQmsLuMF7olr9OaTaR26WjwJWv4kYz5JakPSmgFQy7NhpuCBXaLebRmKHa1vfKdNlLrIUghVJSKuVtEfHAnLhlbZo47AY4-dhZ8SMj_Rj1aC0lyrwn1GLDDeTFoQpIZAmkO-44ho_t6mBBm3YoPQ8xfugoEGeHNuUuP6rwOAXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mg

Re: [Freesurfer] Freeview does not show images

[Justina Lee]

External Email - Use Caution

Hi  Ruopeng,

I tried to run the glxgears command in the WSL Ubuntu subsystem, but it
doesn't show me the gears. I am having the same issue as this thread linked
here: 
https://secure-web.cisco.com/1_nwpKy6edOMjc8Fb4TT_DQsKayIHq7yz6rjZXWYrhXvOMtkPtnDTAgvyHwlJknIz0NqjN44E48l9HTzHWpxTRB7K9qfWEddgLzY-N8DwQ9LJuanknR3cqBZCSGGybx3kfCwXL0JqnlBMKd4YPRiOBQ0tvJnklmkeHvAu0bOaW_5y3ABUG-9zqwhYo-JKOs-npIB2AdvV4eRkQ6-M0I8iPV2U8PHw1JoFhE100pzdpkEHDewV_Z7VJaoHYTWjJR4LPr_DMg2vecc2aM_SIu4Zgmk3bNNQ0II7UXChxgZatN8b6T1b4ayMSM8cKseJiDTbEG_czfPEz8ArXDVdM5yDMQ/https%3A%2F%2Fgithub.com%2Fmicrosoft%2Fwslg%2Fissues%2F654
 I followed the advice
and downloaded the latest Intel Graphics Driver, but this did not seem to
fix the issue for me.

I also looked at the corresponding debian package installer in accordance
with my ubuntu version, and the same error occurs. How can I add a 3D
accelerator or GPU acceleration so that the glxgears command can show me
the gears?

Thanks for your help and time.

Sincerely,
Justina

On Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng  wrote:

> Are you able to run glxgears command? Do you see spinning gears?
>
> Ruopeng
>
> On Oct 6, 2022, at 4:28 AM, Justina Lee  wrote:
>
> External Email - Use Caution
>
> To whom this may concern and can help,
>
> I am currently trying to run Freeview under the Windows Subsystem Linux
> System. I can successfully download and open images, but nothing seems to
> be showing on my end (see image attached at the end).
>
> In order to find out what is preventing the X-server from correctly
> displaying graphics, I have tried to run the $ xeyes command and the eyes
> pop up, meaning that the X-windows server is working fine.
>
> Upon checking the WSL Version, I am currently using the WSL version 2.
>
> I have entered the two commands as follows:
>
> $ *echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc*
> $ *echo "export DISPLAY=:0" >> $HOME/.bashrc*
> Then I exited Ubuntu, and tried to run freeview again (attempting to open
> a data file T1.mgz.) This still did not produce any image in freeview,
> although it opened it up. I tried changing the window, contrast, and
> brightness but to no avail.
>
> Is there another solution?
>
> Terribly sorry and thank you so much for your time.
>
> Sincerely,
> Justina
> 
> ___
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The information in this e-mail 

[Freesurfer] Virtual Machine password

[Justina Lee]

External Email - Use Caution

To whom it may concern,

I am currently installing the Virtual Machine to run Freesurfer. I was
prompted with a password and was wondering if anyone could share with me
the password.

Thank you for your help and time.

Sincerely,
Justina
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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