External Email - Use Caution
Yes, actually I have the environment already set up, please see below:
When I open the terminal I get:
Last login: Fri Jul 16 16:46:38 on ttys000
-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /Applications/freesurfer/7.1.1
FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects
MNI_DIR /Applications/freesurfer/7.1.1/mni
FSL_DIR /usr/local/fsl
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://secure-web.cisco.com/1WEadXG3F4w1FQJa33A2XiN6jF_wxb9o70FOn-XzzBpet4f....
When I type freeview, I get:
BT136080:~ bajsah$ freeview
/Applications/freesurfer/7.1.1/bin/freeview: line 2: 8086 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
When I type which freeview and --help, I get:
BT136080:~ bajsah$ which freeview
/Applications/freesurfer/7.1.1/bin/freeview
BT136080:~ bajsah$ freeview --help
Usage: freeview [OPTION ARGUMENT:SUB-OPTION]...
Volume and surface viewer and editor for freesurfer.
-v, --volume <FILE>...
Load one or multiple volume files. Available sub-options are:
...
...
Screenshot for the above stuff is attached below:
[image: Screen Shot 2021-07-16 at 7.34.20 PM.png]
On Fri, Jul 16, 2021 at 6:49 PM fsbuild fsbuild@contbay.com wrote:
Just wondering if you already tried using bash to setup the environment.
- R.
%] bash bash-3.2$ export FREESURFER_HOME=/Applications/freesurfer/7.1.1 bash-3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.1.1 FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects
bash-3.2$ which freeview /Applications/freesurfer/7.1.1/bin/freeview bash-3.2$ freeview --help . . . output deleted . . . . . . if that succeeds then see if freeview will open an empty window . . . bash-3.2$ freeview
On Jul 16, 2021, at 17:33, Sahil Bajaj sahil.brain@gmail.com wrote:
External Email - Use CautionHi Ruopeng
Thanks for your quick response.
If I use that I still get the similar error:
BT136080:~ bajsah$ $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview Segmentation fault: 11Segmentation fault: 11
Sahil
On Fri, Jul 16, 2021 at 1:23 PM Wang, Ruopeng RWANG4@mgh.harvard.edu wrote:
What if you run:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview -f fsaverage/surf/lh.inflated
On Jul 16, 2021, at 1:07 PM, Sahil Bajaj sahil.brain@gmail.com wrote:
External Email - Use CautionHi everyone,
I am having following error while opening freeview in terminal:
BT136080:01_Project_FreeSurfer bajsah$ freeview -f
fsaverage/surf/lh.inflated
/Applications/freesurfer/7.1.1/bin/freeview: line 2: 27046 Segmentation
fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Somehow, this was working fine a few weeks ago, but I can't open
freeview now. I double checked the folder: /Applications/freesurfer/7.1.1/bin/freeview and everything seems to be at place.
Any suggestions/tips to resolve this, please?
Thanks a lot ! Sahil _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from
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