External Email - Use Caution        


Hello Priya,

It could help to know,
- the version of freesurfer you installed, e.g., the latest 7.3.2 release from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/rel7downloads
- if you used the pkg installer file, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.3.2/freesurfer-darwin-macOS-7.3.2.pkg
- what version of MacOS you are running
- if you are on an Intel Mac or a new Mac with an M1 or M2 chip.

Please make sure you have registered and obtained the freesurfer license.txt file by filling out the form, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/registration.html

The thread you referenced, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://neurostars.org/t/problem-installing-freesurfer-in-mac/20552/21, showed the crash went away for a user with a MacBook Pro if they unplugged their external monitor.  This is - or at least was - a known problem with a 2nd monitor causing a segfault when trying to run some graphics programs.  So try unplugging any external monitor if you are using a Mac laptop.

I would try explicitly running the bash shell in your terminal window, but typing “bash” at the terminal prompt.  You should then see the output,

$ bash

The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit https://support.apple.com/kb/HT208050.
userid@hostname:~>

You can then set FS_LICENSE in your environment to point to the license.txt file.  You can put license.txt in your home directory, e.g., wherever that path is,

userid@hostname:~> echo $HOME
/Users/priya
userid@hostname:~> export FS_LICENSE=$HOME/license.txt
userid@hostname:~> cat $FS_LICENSE
< output deleted - just make sure the environment variable points to license.txt >

Then setup the fressurfer environment, e.g., for the 7.3.2 release installed with the .pkg file,

userid@hostname:~> export FREESURFER_HOME=/Applications/freesurfer/7.3.2
userid@hostname:~> source $FREESURFER_HOME/SetUpFreeSurfer.sh

-------- freesurfer-darwin-macOS-7.3.2-20220803-878457d --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME       /Users/developer/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Users/developer/freesurfer/subjects
TUTORIAL_DATA     /Users/developer/tutorial_data
MNI_DIR           /Users/developer/freesurfer/mni
WARNING: /Users/developer/freesurfer/fsl_507/bin does not exist.
FSL_DIR           /Users/developer/freesurfer/fsl_507

userid@hostname:~> which freeview
/Applications/freesurfer/7.3.2/bin/freeview

… try running freeview with no argument to see if it brings up an empty window …

userid@hostname:~> freeview

… try displaying a simple volume …

userid@hostname:~> freeview $SUBJECTS_DIR/bert/mri/brain.mgz

Let us know how it goes.

- R.

On Oct 5, 2022, at 03:11, priya padma <priya@phenomx.ai> wrote:

        External Email - Use Caution        


Hello Team,

I just installed freesurfer and freeview using the methods mentioned in 
the installation was successful and after creating the environment the freeview also opened but whenever I open any volume, freeview crashes and I get an error saying line 2:  6736 Segmentation fault: 11  $FREESURFER_HOME/Freeview..app/Contents/MacOS/freeview "$@"

and tried to move the terminal to the main laptop screen but still I get the same error. I am unable to open the sample data given along with freesurfer.

Could you help me with this issue?

-- 
Best Regards
Padma Priya
AI Developer 

PhenoMx, Inc.
priya@phenomx.ai | (+82)10-5405-2685


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