Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1
Fressurfer version 7.4.0
XQuatz 2.8.5
licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)
environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given:
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file:
freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna
External Email - Use Caution
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf>
External Email - Use Caution
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way.
I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Wang, Ruopeng" RWANG4@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf> External Email - Use Caution
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il...
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution
Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way. I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf> External Email - Use Caution
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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/freesurferhttps://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il3jxFy101naM-yIxvXqpP2HyIp-eGB9RvrusOKbKf9XRXAN55tTbtdwTjP9dePStqI5NKRTIAsPPY6kJCfItER09-PaaHsooudqs_kiKeXxx9OrieieJPMPBxG5dmGT1GrY9s8bK8r1SYNmjTW7Z5IckX9mnkBlpxYMS97B8lnTFbjQj_BXa0Ya7vv7IcJqIbM1InBbPxGvF7ToPyG4Rzy-r98xWDbyFexID6H8dkhLe_yHX7HhwFJDKMTfV5ZsfIQ5KGVzR-HCeEIAP5S4_HVTTDoacjsxxjrOd1OcYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It’s there:
licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)
Or do you mean /Applications/freesurfer/license.txt?
Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Wang, Ruopeng Gesendet: Freitag, 3. Januar 2025 16:58 An: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] [ext] Re: Freeview crash
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.de mailto:anna.tietze@charite.de > wrote:
External Email - Use Caution
Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way.
I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edu mailto:RWANG4@mgh.harvard.edu > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.de mailto:anna.tietze@charite.de > wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1
Fressurfer version 7.4.0
XQuatz 2.8.5
licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)
environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given:
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file:
freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna
<problem report freeview.rtf>
External Email - Use Caution
_______________________________________________ Freesurfer mailing list mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il3jxFy101naM-yIxvXqpP2HyIp-eGB9RvrusOKbKf9XRXAN55tTbtdwTjP9dePStqI5NKRTIAsPPY6kJCfItER09-PaaHsooudqs_kiKeXxx9OrieieJPMPBxG5dmGT1GrY9s8bK8r1SYNmjTW7Z5IckX9mnkBlpxYMS97B8lnTFbjQj_BXa0Ya7vv7IcJqIbM1InBbPxGvF7ToPyG4Rzy-r98xWDbyFexID6H8dkhLe_yHX7HhwFJDKMTfV5ZsfIQ5KGVzR-HCeEIAP5S4_HVTTDoacjsxxjrOd1OcYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitV...
_______________________________________________ Freesurfer mailing list mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitVjyVeHTdGRVTyOgmTpiCikQDZWiFccCRyhtW_q_C3nlwIEgjD_S4xBcegNL4wFTlj9DY7PSanZGnfTTMPaigtNE89HaUY3bMazDc2VUtm0-zzcnx5xUYw-BSmO7AIPjOd97McD1sMCWlCXNeqalX98VmbZdCqT1VBdwtam8sY3ZCnp8h4GgZ8CQPmYdAFWhnW8ErSl3nRNKIVT6oflvJ79MigCrt8VcFVJonMLnKXigZ5_wNg_TuteqpSrwrStpy4THTu7x47gf70NU9uz3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitV...
External Email - Use Caution
It’s there:
licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)
Or do you mean /Applications/freesurfer/license.txt?
Von: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > Im Auftrag von Wang, Ruopeng Gesendet: Freitag, 3. Januar 2025 16:58 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Betreff: Re: [Freesurfer] [ext] Re: Freeview crash
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.de mailto:anna.tietze@charite.de > wrote:
External Email - Use Caution
Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way.
I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu > on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edu mailto:RWANG4@mgh.harvard.edu > Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu > Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.de mailto:anna.tietze@charite.de > wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1
Fressurfer version 7.4.0
XQuatz 2.8.5
licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works)
environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given:
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file:
freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz
/Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna
<problem report freeview.rtf>
External Email - Use Caution
_______________________________________________ Freesurfer mailing list mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/16k7GeT10xnyGxKgd_FlVZCkydV-RDVkVN5jCKeQIWh34il3jxFy101naM-yIxvXqpP2HyIp-eGB9RvrusOKbKf9XRXAN55tTbtdwTjP9dePStqI5NKRTIAsPPY6kJCfItER09-PaaHsooudqs_kiKeXxx9OrieieJPMPBxG5dmGT1GrY9s8bK8r1SYNmjTW7Z5IckX9mnkBlpxYMS97B8lnTFbjQj_BXa0Ya7vv7IcJqIbM1InBbPxGvF7ToPyG4Rzy-r98xWDbyFexID6H8dkhLe_yHX7HhwFJDKMTfV5ZsfIQ5KGVzR-HCeEIAP5S4_HVTTDoacjsxxjrOd1OcYw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/13F2gxxp3c-FwjfGSH5Mf2BBQV-8Ts9VuLTvomqjjdqv6AW...
_______________________________________________ Freesurfer mailing list mailto:Freesurfer@nmr.mgh.harvard.edu Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1QJz6xShsji1s-ybZT93kuMT6Br9o_orKDeEAjsEP1AQitVjyVeHTdGRVTyOgmTpiCikQDZWiFccCRyhtW_q_C3nlwIEgjD_S4xBcegNL4wFTlj9DY7PSanZGnfTTMPaigtNE89HaUY3bMazDc2VUtm0-zzcnx5xUYw-BSmO7AIPjOd97McD1sMCWlCXNeqalX98VmbZdCqT1VBdwtam8sY3ZCnp8h4GgZ8CQPmYdAFWhnW8ErSl3nRNKIVT6oflvJ79MigCrt8VcFVJonMLnKXigZ5_wNg_TuteqpSrwrStpy4THTu7x47gf70NU9uz3/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/13F2gxxp3c-FwjfGSH5Mf2BBQV-8Ts9VuLTvomqjjdqv6AW...
External Email - Use Caution
I mean /Applications/freesurfer/license.txt.
On Jan 3, 2025, at 11:36 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
It’s there: licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) Or do you mean /Applications/freesurfer/license.txt?
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Wang, Ruopeng Gesendet: Freitag, 3. Januar 2025 16:58 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] [ext] Re: Freeview crash
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way. I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf> External Email - Use Caution
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Hi Ruopeng,
It works with the app when I move the licence.txt! It doesn’t work from the terminal so far, but this helps a lot. Thank you very much!
Best, Anna
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Wang, Ruopeng" RWANG4@MGH.HARVARD.EDU Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Friday, 3. January 2025 at 18:17 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [ext] Re: Freeview crash
I mean /Applications/freesurfer/license.txt.
On Jan 3, 2025, at 11:36 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
It’s there: licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) Or do you mean /Applications/freesurfer/license.txt?
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Wang, Ruopeng Gesendet: Freitag, 3. Januar 2025 16:58 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] [ext] Re: Freeview crash
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way. I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf> External Email - Use Caution
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You can run freeview from the the command-line by directly calling the binary in the app bundle, for example:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 3, 2025, at 3:58 PM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution
Hi Ruopeng,
It works with the app when I move the licence.txt! It doesn’t work from the terminal so far, but this helps a lot. Thank you very much!
Best, Anna
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 3. January 2025 at 18:17 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [ext] Re: Freeview crash
I mean /Applications/freesurfer/license.txt.
On Jan 3, 2025, at 11:36 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
It’s there: licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) Or do you mean /Applications/freesurfer/license.txt?
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Wang, Ruopeng Gesendet: Freitag, 3. Januar 2025 16:58 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] [ext] Re: Freeview crash
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way. I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf> External Email - Use Caution
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Hello Ruopeng,
Just FYI - users should no longer have to put a license.txt under the freesurfer distribution; that fallback location should remain for backwards compatibility with old freesurfer setups. Apps/commands should first always check if FS_LICENSE is set in the environment and test if it points to a valid license.txt file. We added that so users do not need to sudo, and add the freesurfer license under the distribution every time they (re)install freesurfer, or if they want to have multiple versions of freesurfer installed, so a single license file location pointed to by FS_LICENSE works for different/multiple installs of freesurfer.
- rob
On Jan 3, 2025, at 17:32, Wang, Ruopeng RWANG4@mgh.harvard.edu wrote:
You can run freeview from the the command-line by directly calling the binary in the app bundle, for example:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 3, 2025, at 3:58 PM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution
Hi Ruopeng,
It works with the app when I move the licence.txt! It doesn’t work from the terminal so far, but this helps a lot. Thank you very much!
Best, Anna
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@MGH.HARVARD.EDUmailto:RWANG4@MGH.HARVARD.EDU> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Friday, 3. January 2025 at 18:17 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [ext] Re: Freeview crash
I mean /Applications/freesurfer/license.txt.
On Jan 3, 2025, at 11:36 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
It’s there: licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) Or do you mean /Applications/freesurfer/license.txt?
Von: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> Im Auftrag von Wang, Ruopeng Gesendet: Freitag, 3. Januar 2025 16:58 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] [ext] Re: Freeview crash
To run as an app bundle, since there is no global environment settings, you need to put the license file in /Applications/freesurfer folder. Then you should be able to load data.
On Jan 3, 2025, at 12:47 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
External Email - Use Caution Yes, I’ve tried that as well. Freeview opens as an app bundle, but it crashes when I load a file. Interestingly, this is inconsistent—sometimes I can load a file without any issues, but most of the time, it crashes in the same way. I’ve this problem on two different Macs:
* System 1: macOS Sonoma 14.5 with FreeSurfer 7.3.2. * System 2: macOS Sonoma 14.7.1 with FreeSurfer 7.4.0.
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wang, Ruopeng" <RWANG4@mgh.harvard.edumailto:RWANG4@mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, 2. January 2025 at 19:04 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [ext] Re: [Freesurfer] Freeview crash
Have you tried running freeview as an app bundle? Or can you try running freeview directly from the binary location? Like this:
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
On Jan 2, 2025, at 7:14 AM, Tietze, Anna <anna.tietze@charite.demailto:anna.tietze@charite.de> wrote:
Hi,
When I want to open files with freeview, it crashes immediately. I tried my own recon-all output and the bert dataset. Can you help me?
Operating system: Mac, Sonoma 14.7.1 Fressurfer version 7.4.0 XQuatz 2.8.5 licence.txt located in: /Applications/freesurfer/7.4.0/license.txt (can be read, as recon-all works) environment is set by FREESURFER_HOME=/Applications/freesurfer/7.4.0 and source $FREESURFER_HOME/SetUpFreeSurfer.sh
When I run the command freeview, the following message is given: /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6615 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Or trying to open a file: freeview -v /Users/annatietze/Documents/freesurfer/freesurfer_subjects/nini_ra/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6765 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
freeview -v /Applications/freesurfer/7.4.0/subjects/bert/mri/orig/001.mgz /Applications/freesurfer/7.4.0/bin/freeview: line 2: 6799 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
Attached is a detailed error report.
What did I overlook?? Thank you so much for help!
Best, Anna <problem report freeview.rtf> External Email - Use Caution
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Dicamillo, Robert -
Tietze, Anna -
Wang, Ruopeng