External Email - Use Caution        


It looks like you did not use the .pkg file installer to install Freesurfer on the Mac, otherwise you would have a path like /Applications/freesurfer/7.4.1 to use as FREESURFER_HOME.  The installer should ensure the privileges should be correct to run commands.   There are several 7.X freesurfer releases, but the latest release is 7.4.1 and you can download it via the link, e.g.,

https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-macOS-darwin_x86_64-7.4.1.pkg

I would first remove what you have on your system from the terminal window with,

$ sudo rm -rf /Applications/freesurfer

Then in a Finder Window navigate to the Downloads folder (or to wherever you downloaded freesurfer-macOS-darwin_x86_64-7.4.1.pkg).  You should be able to RIGHT CLICK on that file, select open with the default pkg installer, and then enter your password etc. to install it.  Right clicking should bypass having to do some of the security exemptions in system preferences.

Once the install is complete, setup the Freesurfer environment in the terminal window,

$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.4.1
FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjects
MNI_DIR           /Applications/freesurfer/7.4.1/mni

You also need a license file, license.txt.  Once you complete the license request form at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/registration.html you will receive a file “licesne.txt” via the email address used in the form.   Download/copy the license.txt file to your machine from the email.

If your home directory is for example /Users/hyejung then you will see the following in the terminal window,

$ cd
$ pwd
/Users/hyejung
$ echo $HOME
/Users/hyejung

… if you downloaded license.txt into your Download folder ...

$ cd Downloads
$ ls license.txt
license.txt
$ cp -p -f  license.txt  $HOME/.
$ cd $HOME
$ ls license.txt
license.txt

You could also use the Finder to navigate and drag/drop the license.txt into your home directory.   Once it it there, set the environment variable FS_LICENSE so freesurfer commands will find the license when they run,

$ export FS_LICENSE=$HOME/license.txt

Then it should work to run freesurfer commands from the terminal window including freeview.

- R.


On Jan 16, 2024, at 20:47, 윤혜정 <hyejung7890@amc.seoul.kr> wrote:

        External Email - Use Caution        

Good day.

When I run recon-all for my nii files I get either one of the following error messages:

1. ERROR: could not configure recon-all parameters Killed 

2. ERROR: could not configure recon-all parameters 
/Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: cannot execute binary file 
/Applications/freesurfer/bin/fspython: line 20: /Applications/freesurfer/python/bin/python3: Undefined error: 0

Or 

3. a Pop Up message "_struct.cpython-38-darwin.so" cannot be opened because the developer cannot be verified. 
mac OS cannot verify that this app is free from malware. 

I googled the third error message and tried "Allow anyways" from the privacy setting. Then the next message pops up, then the next and the next. 

Could you please help me to understand the cause of the above 3 error messages? 
I tried to redownload freesurfer as well as python but none worked. 

Thank you in advance. 

Best,
Alice

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