External Email - Use Caution
Please try the following: 1) Open a new terminal window and run the bash shell as, $ arch -arm64 /bin/bash
2) set FS_LICENSE to point to your license.txt file. Say it is in your home directory, e.g., $HOME/license.txt. It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read. $ ls $HOME/license..txt/Users/<your userid>/license.txt$ export FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou@youremail.something <— email you used to register with 3) setup the environment $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ 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 /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects MNI_DIR /Applications/freesurfer/7.3.2/mni
4) Try running freeview w/o any arguments to see if it opens an empty window. $ freeview 5) If that worked, quit freeview and then try running freeview to open one of the provided volumes in the 7.3.2 release, $ freeview $SUBJECTS_DIR/bert/mri/brain.mgz 5) If that worked, then try running freeview on your file again. - R.
Thank you. I tried the steps and it worked once.
Now I try opening the file and it keeps crushing The only file that opens now without crushing is “freeview $SUBJECTS_DIR/bert/mri/brain.mgz”
Reuben A.
From: fsbuild fsbuild@contbay.com Date: Thursday, December 15, 2022 at 12:14 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Addison, Reuben RAddison@MGHIHP.EDU Subject: Re: [Freesurfer] Freeview quit unexpectedly
External Email - Use Caution
Please try the following:
1) Open a new terminal window and run the bash shell as,
$ arch -arm64 /bin/bash
2) set FS_LICENSE to point to your license.txt file. Say it is in your home directory, e.g., $HOME/license.txt. It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read.
$ ls $HOME/license.txt /Users/<your userid>/license.txt $ export FS_LICENSE=$HOME/license.txt $ head -1 $FS_LICENSE you@youremail.somethingmailto:you@youremail.something <— email you used to register with
3) setup the environment
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ 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 /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects MNI_DIR /Applications/freesurfer/7.3.2/mni 4) Try running freeview w/o any arguments to see if it opens an empty window.
$ freeview
5) If that worked, quit freeview and then try running freeview to open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
5) If that worked, then try running freeview on your file again.
- R.
Please ignore the previous email. Apparently when I type the command it works but the issue is with using the gui
Reuben A.
Get Outlook for iOShttps://aka.ms/o0ukef ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Addison, Reuben RAddison@mghihp.edu Sent: Friday, December 16, 2022 10:02:56 AM To: fsbuild fsbuild@contbay.com; freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freeview quit unexpectedly
Thank you.
I tried the steps and it worked once.
Now I try opening the file and it keeps crushing
The only file that opens now without crushing is “freeview $SUBJECTS_DIR/bert/mri/brain.mgz”
Reuben A.
From: fsbuild fsbuild@contbay.com Date: Thursday, December 15, 2022 at 12:14 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Addison, Reuben RAddison@MGHIHP.EDU Subject: Re: [Freesurfer] Freeview quit unexpectedly
External Email - Use Caution
Please try the following:
1) Open a new terminal window and run the bash shell as,
$ arch -arm64 /bin/bash
2) set FS_LICENSE to point to your license.txt file. Say it is in your home directory, e.g., $HOME/license.txt. It can be anywhere but you just have to set FS_LICENSE to its absolute path and test it can be read.
$ ls $HOME/license.txt
/Users/<your userid>/license.txt
$ export FS_LICENSE=$HOME/license.txt
$ head -1 $FS_LICENSE
you@youremail.somethingmailto:you@youremail.something <— email you used to register with
3) setup the environment
$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2
$ 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 /Applications/freesurfer/7.3.2/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.3.2/subjects MNI_DIR /Applications/freesurfer/7.3.2/mni
4) Try running freeview w/o any arguments to see if it opens an empty window.
$ freeview
5) If that worked, quit freeview and then try running freeview to open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
5) If that worked, then try running freeview on your file again.
- R.
freesurfer@nmr.mgh.harvard.edu
-
Addison, Reuben -
fsbuild