Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

[fsbuild]

External Email - Use Caution

When you say you are running Mojave, I think you probably meant to write 
10..14.6 (not 10.16.6).
You could check you have the latest version of XQuartz (2.8.5) installed 
from,https://secure-web.cisco.com/11eALbuyxL0_txSil8AchFZPgix3GCpAuJbqcYDFJFtJt6F-kBaf9JU5a338EKemH6N8VWFBwwDAwLWuuQJkh2SpdmbjcCUa76MdxUsBf1e_Cn3t1OtIUBfxrHP25IKD9WR6MAbUjPnX32kYdki8uhdNtqBeX1ROEXkPb3jlB_CZmEhuI3qIaYUx6FLN0oI9P6qQpP8MfUn1MD-hv2gomxH2sQkzNtqWuw6oLLHKAQxmo4cFHuvYa709L7ZZ0Qi89X11sEtAAVLwbOgucQ-Aon2ovVKDrSd9ZWLsERG05Q--yi2OKSN1wvIzUiHNQbzBQSeuSsxJ0-cy4wI8tCvNDwQ/https%3A%2F%2Fwww.xquartz.org%2F
You may need to reboot the machine after installing Xquartz.
Once back up, open a new terminal window and run the bash shell,
$ bash
Try putting your license file, e.g., license.txt. in your $HOME directory, and 
then set the environment variable FS_LICENSE to its absolute path, e.g.
$ cd $HOME$ head -1 license.tx...@somewhere.org.  <—— email address you 
used to register with
$ export FS_LICENSE=$HOME/license.txt$ head -1 $fs_licens...@somewhere.org. 
 <—— email address you used to register with
Then the usual setup,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ 
source $FREESURFER_HOME/SetUpFreeSurfer.sh
Then try opening an empty Freeview window again,$ freeview
- R.
On Feb 8, 2023, at 14:28, Rankin McGugin  
wrote:
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

[Wang, Ruopeng]

Can you try the latest dev build from here?
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Ruopeng

On Feb 8, 2023, at 2:28 PM, Rankin McGugin 
mailto:rankin.mcgu...@gmail.com>> wrote:


External Email - Use Caution

of course, see attached



Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644


On Wed, Feb 8, 2023 at 1:22 PM Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>> wrote:
Would it be possible to send us the full crash report? You can find it in the 
Console app.

Best,
Ruopeng

On Feb 8, 2023, at 1:48 PM, Rankin McGugin 
mailto:rankin.mcgu...@gmail.com>> wrote:


External Email - Use Caution

Here is my error log:

Last login: Wed Feb  8 12:03:23 on ttys000
Rankins-MacBook-Pro:~ rankinmcgugin$ export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2
Rankins-MacBook-Pro:~ rankinmcgugin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR   /Applications/freesurfer/7.3.2/mni
Rankins-MacBook-Pro:~ rankinmcgugin$
Rankins-MacBook-Pro:~ rankinmcgugin$ which freeview
/Applications/freesurfer/7.3.2/bin/freeview
Rankins-MacBook-Pro:~ rankinmcgugin$ freeview
/Applications/freesurfer/7.3.2/bin/freeview: line 2:  1592 Segmentation fault: 
11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Rankins-MacBook-Pro:~ rankinmcgugin$



Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644


-- Forwarded message -
From: Rankin McGugin mailto:rankin.mcgu...@gmail.com>>
Date: Wed, Feb 8, 2023 at 12:47 PM
Subject: Freeview 'quit unexpectedly' before opening
To: mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello,

I am a longtime FS user. I have read threads on this topic but no suggestions 
work in my case.  I have the license file in place. I removed my previous 
version of FS and have updated to 7.3.2.  However, now when I try to start 
Freeview, I get this problem report before the app even opens:

I have tried downloading the standalone Freeview, but get the same error.  I 
have restarted the computer, completely removed everything and redownloaded it, 
but still the same issue persists.
I am using macOS Mojave, 10.16.6
Are you able to guide me how to fix this and open Freeview?

Thank you!

Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644
___
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

___
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

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

[Wang, Ruopeng]

Would it be possible to send us the full crash report? You can find it in the 
Console app.

Best,
Ruopeng

On Feb 8, 2023, at 1:48 PM, Rankin McGugin 
mailto:rankin.mcgu...@gmail.com>> wrote:


External Email - Use Caution

Here is my error log:

Last login: Wed Feb  8 12:03:23 on ttys000
Rankins-MacBook-Pro:~ rankinmcgugin$ export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2
Rankins-MacBook-Pro:~ rankinmcgugin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME   /Applications/freesurfer/7.3.2/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.3.2/subjects
MNI_DIR   /Applications/freesurfer/7.3.2/mni
Rankins-MacBook-Pro:~ rankinmcgugin$
Rankins-MacBook-Pro:~ rankinmcgugin$ which freeview
/Applications/freesurfer/7.3.2/bin/freeview
Rankins-MacBook-Pro:~ rankinmcgugin$ freeview
/Applications/freesurfer/7.3.2/bin/freeview: line 2:  1592 Segmentation fault: 
11  $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Rankins-MacBook-Pro:~ rankinmcgugin$



Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644


-- Forwarded message -
From: Rankin McGugin mailto:rankin.mcgu...@gmail.com>>
Date: Wed, Feb 8, 2023 at 12:47 PM
Subject: Freeview 'quit unexpectedly' before opening
To: mailto:freesurfer@nmr.mgh.harvard.edu>>


Hello,

I am a longtime FS user. I have read threads on this topic but no suggestions 
work in my case.  I have the license file in place. I removed my previous 
version of FS and have updated to 7.3.2.  However, now when I try to start 
Freeview, I get this problem report before the app even opens:

I have tried downloading the standalone Freeview, but get the same error.  I 
have restarted the computer, completely removed everything and redownloaded it, 
but still the same issue persists.
I am using macOS Mojave, 10.16.6
Are you able to guide me how to fix this and open Freeview?

Thank you!

Rankin W. McGugin, PhD
Research Assistant Professor
Department of Psychology
Vanderbilt University
email: rankin.mcgu...@vanderbilt.edu
work phone: (615) 322-4644
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] freeview quit unexpectedly on Mac OS M1

[fsbuild]

External Email - Use Caution

Please try the following with the latest 7.3.2 release.  The release page 
is https://secure-web.cisco.com/19K4NxhUlkogZZJ6mlyOImaI2Y4zmXjc6dwibN7nIQsfe_lWxinx40Flxvt9NeD5PMIt1r22ojFGIVQ1V-4Pb5nXsf43uRLNcvEq3QUVVNGyMjhCE8aoZmd-PLKwM9S0t5jcIBbw275wC0OF4OVV9QvWqkGRb65ofEj0Y3FuorMiG2bM8Gm1JDclitrKVNlGjXyOxE2G1wVVHF9W1ggVMQtkB7yooZle77Tp4dPP5Tq1ZpwXb5Zc46RWSryn1r55rnwlmfob_w_N5NBN8j878dj4Rak7e13PGX7hQWkR6Sr4sFdY_GuC7QWz6hN9eFpz0bppmyZdL01yljWsAOoQNfw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads%26nbsp;and
 the link to the .pkg file 
is https://secure-web.cisco.com/1Wx2_5nhoR76Fau-VOEeMoQVIQIDXjamvDF-EFBcqQyt6f80bHsZHLkjkoNhP2bb53qYGAHwFjCvIC6OKEfTYiXngx9HRC8FN9UtODT1c6OVwjwITwjAKua7h0Hd76ZwrN9_2Qj8awhCLQiWAMNEWoOn5G-yf8uB6A-z_Hj2G7LkBEjutSbSzjUc8QN20QSPu_xsfCI0RZT1LaBN79_RH-Yqgux6hILnLhtWzJ1E2De_kR_rgHRiXPFg06OE-HIoau12weC-viiokCAojj4oGPoCdUS8oE58tnJ3nsSuMWTMhy587XGiS49N1qqe2XpzEyOXChssxytV28DzVSAO5Fg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer-darwin-macOS-7.3.2.pkg
1) Install the 7.3.2 release listed above.  It will be installed as 
/Applications/freesurfer/7.3.2
2)  Open a new terminal window and run the bash shell as,
$ arch -arm64 /bin/bash
3) Set FS_LICENSE to point to the license.txt file you downloaded after 
registering via the online form at 
https://secure-web.cisco.com/12TyPaJsjD6Q9mekQ3_jITFFbb2NrPRGCuk6aPL36fn1jheifoCfpGcSh1bw_WNdv4w4aLnuF6w0RDVne_ZMB-wHfjj1UQVf3zoKRzSQ9cBy_KM4TWxF6LN0QDfvUFadZnhn9wQ_qcIb3gu0ObbL01LxCN-29321oF7Sf3_WMkF8pXPEJblhbNePWgZ0lVxwYUGhpEEgkBupUrQ_2oqaoNJOij-nG3eLVKYz-mJ58PxbTNBK536TrzWWSFAzrt2mJ4wUX97kn-995k2RSXhakecmfDVCHPAq-j1X7ph4CAW2sMitK-5JZtyhRumobhFbMt2yjXXE9QqNtAThYZkVPvw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
  For example, it could be in your home directory as $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 $HOME/license.txt/Users//license.txt$ export 
FS_LICENSE=$HOME/license.txt$ head -1 $FS_LICENSEyou@youremail.something  
   <— email you used to register with
4) 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/7.3.2FSFAST_HOME  
     /Applications/freesurfer/7.3.2/fsfastFSF_OUTPUT_FORMAT 
nii.gzSUBJECTS_DIR    
  /Applications/freesurfer/7.3.2/subjectsMNI_DIR     
      /Applications/freesurfer/7.3.2/mni
5) Try running freeview from the command line w/o any arguments to see if it 
opens an empty window,
$ freeview
6)  If that worked, quit freeview and then run freeview from the command 
line again to open one of the provided volumes in the 7.3.2 release,
$ freeview $SUBJECTS_DIR/bert/mri/brain.mgz
7) If that worked, then try running freeview from the command line on one of 
your own volume or surface files.
- R.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[Wang, Ruopeng]

After you load the image from the command-line, can you then load more images 
from the GUI?

Ruopeng

On Dec 20, 2022, at 3:23 AM, Addison, Reuben 
mailto:raddi...@mghihp.edu>> wrote:

The answer to this is question ‘ opening an image from the gui ‘ is yes. The 
image only opens when I open from the command line

Reuben A.

Get Outlook for iOS<https://aka.ms/o0ukef>

From: fsbuild mailto:fsbu...@contbay.com>>
Sent: Tuesday, December 20, 2022 7:56:12 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Cc: Addison, Reuben mailto:raddi...@mghihp.edu>>
Subject: Re: [Freesurfer] Freeview quit unexpectedly


External Email - Use Caution


By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI 
Open-> pull down menu that you get the core dump listed below, but it works 
when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command 
line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your program/command can 
remedy this,

$ bash
$ export MallocNanoZone=0 && freeview

- but this may not work.   I don’t see any other workarounds for this right 
now.  I have not seen this error before with freeview on older versions of 
MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben 
mailto:raddi...@mghihp.edu>> wrote:

I updated the Xquartz yet still same issue. Freeview only works with the 
command line but the gui is till crashing.

Gkxgears seems to work fine

I have attached images of both the crash report and the graphics information 
about my mac.

Reuben A


​
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[Addison, Reuben]

The answer to this is question ‘ opening an image from the gui ‘ is yes. The 
image only opens when I open from the command line

Reuben A.

Get Outlook for iOS<https://aka.ms/o0ukef>

From: fsbuild 
Sent: Tuesday, December 20, 2022 7:56:12 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
Subject: Re: [Freesurfer] Freeview quit unexpectedly


External Email - Use Caution

By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview GUI 
Open-> pull down menu that you get the core dump listed below, but it works 
when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from the command 
line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your program/command can 
remedy this,

$ bash
$ export MallocNanoZone=0 && freeview

- but this may not work.   I don’t see any other workarounds for this right 
now.  I have not seen this error before with freeview on older versions of 
MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben  wrote:

I updated the Xquartz yet still same issue. Freeview only works with the 
command line but the gui is till crashing.

Gkxgears seems to work fine

I have attached images of both the crash report and the graphics information 
about my mac.

Reuben A


​
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[fsbuild]

External Email - Use Caution

By crashing from the GUI do you mean that you when you try to navigate to open 
a file, e.g.,   $SUBJECTS_DIR/bert/mri/brain.mgz,  using the freeview 
GUI Open-> pull down menu that you get the core dump listed below, but it 
works when your run “freeview  $SUBJECTS_DIR/bert/mri/brain.mgz” from 
the command line in the terminal window?

The core dump shows a memory allocation error on MacOSX.  Some postings 
indicate setting MallocNanoZone to zero before running your 
program/command can remedy this,
$ bash$ export MallocNanoZone=0 && freeview
- but this may not work.   I don’t see any other workarounds for this 
right now.  I have not seen this error before with freeview on older 
versions of MacOS, so it may be related to running on MacOS 10.13.

- R.

On Dec 19, 2022, at 14:03, Addison, Reuben  wrote:I 
updated the Xquartz yet still same issue. Freeview only works with the command 
line but the gui is till crashing.  Gkxgears seems to work 
fine I have attached images of both the crash report and the graphics 
information about my mac. Reuben A  ​
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[fsbuild]

External Email - Use Caution

I would downloaded and install the latest Xquartz (X-Windows for MacOS) which 
is version 2.8.3 
from https://secure-web.cisco.com/1opXWtR1b08TpiSxuOjmZYBoO9MYN5pgHsuKLDmoCgQvIQKCE3eLuXMzAhun8yJwDohErdmiN2RaG1_YIuaBUhEqyEnJTavnVvR5HbqS2OIlTNV_aVeIJTge1UvCSpI_itW2lL10W-8V13eDdK_QIOzAeCpiyBwovrfkjBbMkKRHtTbvQg8EvkYE5PXN0VxEqoAPLTUYxEj6y-wSVVShky5YYJjCGFll6x37tCPR245N1zBFv4VFCjqx9iF3A0ogRTe0k___etyob1p0uKc8kUONjzb3L8RpzAgn1rQAZ1U4SCAHbKMHgTqUB9bQSpwoD7ORGeHBOfYHmkcKvFyyk0g/https%3A%2F%2Fwww.xquartz.org%2F%26nbsp;
  This was updated only a week ago and contains universal binaries.
After you install Xquartz open a new terminal window and type “glxgears”. 
 An X-Window should pop up showing the spinning gears.
% which glxgears
/opt/X11/bin/glxgears
% glxgears
303 frames in 5.0 seconds = 60.564 FPS
309 frames in 5.0 seconds = 61.607 FPS
…...
… close glxgears window to exit ...
Then at least your X-Windows graphics will be up to date (which might affect 
the GUI).  Then try your image again.
Do you see any warnings, error, info, etc., listed in the terminal window after 
the freeview command?   If so, please send that along.
Maybe you could send along a screenshot of what “about this mac” displays. 
 That would tell us if you are using a graphics card or the built-in 
graphics - and also a screenshot of the freeview window.
- R.





glxgears.png
Description: Binary data
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[Addison, Reuben]

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 iOS<https://aka.ms/o0ukef>

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Addison, Reuben 

Sent: Friday, December 16, 2022 10:02:56 AM
To: fsbuild ; 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 
Date: Thursday, December 15, 2022 at 12:14 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
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//license.txt

$ export FS_LICENSE=$HOME/license.txt

$ head -1 $FS_LICENSE

you@youremail.something<mailto: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 mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[Addison, Reuben]

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 
Date: Thursday, December 15, 2022 at 12:14 AM
To: freesurfer@nmr.mgh.harvard.edu 
Cc: Addison, Reuben 
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//license.txt
$ export FS_LICENSE=$HOME/license.txt
$ head -1 $FS_LICENSE
you@youremail.something<mailto: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 mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
<https://www.massgeneralbrigham.org/complianceline> .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Freeview quit unexpectedly

[fsbuild]

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 $HOME/license..txt/Users//license.txt$ 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.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.