On Thu, Sep 15, 2022 at 4:00 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu> 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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wighton, Paul <PWIGHTON@mgh.harvard.edu>
Sent: Thursday, September 15, 2022 9:56 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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 000026

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 000026 /home/ylee6/ADIPA_data

You were close with your command "segmentHA_T1.sh 000026 [/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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Thursday, September 15, 2022 7:51 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,

Thank you for your help tremendously throughout this process.

Firstly, attached you will find the requested recon-all.log for the subject 000026 (originally located in the path /home/ylee6/ADIPA_data/000026/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/000026/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=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
WAYLAND_DISPLAY=wayland-0
FMRI_ANALYSIS_DIR=/usr/local/freesurfer/7.3.2/fsfast
MNI_DIR=/usr/local/freesurfer/7.3.2/mni
PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
MNI_PERL5LIB=/usr/local/freesurfer/7.3.2/mni/share/perl5
FREESURFER_HOME=/usr/local/freesurfer/7.3.2
LESSCLOSE=/usr/bin/lesspipe %s %s
LOCAL_DIR=/usr/local/freesurfer/7.3.2/local
TERM=xterm-256color
FIX_VERTEX_AREA=
LESSOPEN=| /usr/bin/lesspipe %s
USER=ylee6
DISPLAY=172.25.144.1:0
SHLVL=1
SUBJECTS_DIR=/usr/local/freesurfer/7.3.2/subjects
XDG_RUNTIME_DIR=/home/ylee6/.xdg
FS_LICENSE=/home/ylee6/license.txt
WSLENV=
XDG_DATA_DIRS=/usr/local/share:/usr/share:/var/lib/snapd/desktop
PATH=/usr/local/freesurfer/7.3.2/bin:/usr/local/freesurfer/7.3.2/fsfast/bin:/usr/local/freesurfer/7.3.2/tktools:/usr/local/freesurfer/7.3.2/mni/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Program Files/MATLAB/R2022a/bin:/mnt/c/Users/lenovo/AppData/Local/Microsoft/WindowsApps:/snap/bin
FSF_OUTPUT_FORMAT=nii.gz
HOSTTYPE=x86_64
PULSE_SERVER=/mnt/wslg/PulseServer
_=/usr/bin/env
OLDPWD=/home/ylee6/ADIPA_data

Finally, I am running the segmentHA_T1.sh command under this pathway:

ylee6@LAPTOP-63HA9ANS:~/ADIPA_data/000026/mri$ segmentHA_T1.sh 000026

resulting in the error that I have shown previously but described again below:

Cannot find wmparc.mgz or norm.mgz or talairach.xfm for the subject.
Has the subject been procesed with recon-all?

I believe that you are right that the SUBJECTS_DIR environment isn't set correctly, so I followed the subjects directory stated in the 'env' command and tried the command again as such:

ylee6@LAPTOP-63HA9ANS:~/ADIPA_data/000026/mri$ segmentHA_T1.sh 000026 [/usr/local/freesurfer/7.3.2/subjects]

Hence resulting in the following commands:

getfullpath: No match.
if: Missing file name.

Could it be that the data from the recon-all for the subject is not in the subject directory but in the other file (ADIPA_data), hence unable to run the command? When I open the folder for subject 00026 on windows, I only find one file in it, which is ' EchoCombination_f02g01_bet.nii.' In this folder under the subject directory stated above (/usr/local/freesurfer/7.3.2/subjects), it does not have the find 'wmparc.mgz,' 'norm.mgz,' or 'talairach.xfm' it needs.

If the problem lies that the files are not in the corresponding folders, could you be able to tell me (as you already know I am a new learning student of linux system) how I can move these files instead of through my computer manually? Does the problem lie somewhere else?

Thank you and I appreciate your time and efforts.

Sincerely,

Justina

On Wed, Sep 14, 2022 at 5:07 PM Wighton, Paul <PWIGHTON@mgh.harvard.edu> wrote:

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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@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 <PWIGHTON@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 2:57 PM
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,

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 <PWIGHTON@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 2:37 PM
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,

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 <PWIGHTON@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 2:28 PM
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,

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 <PWIGHTON@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Justina Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 1:58 PM
To: Freesurfer support list <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 <PWIGHTON@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-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of You Na Lee <justinalee56@gmail.com>
Sent: Tuesday, September 13, 2022 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu <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

Sent from Mail for Windows

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://www.massgeneralbrigham.org/complianceline> .