External Email - Use Caution
Thanks，please don't send emails！
-----原始邮件----- 发件人: freesurfer-request@nmr.mgh.harvard.edu 发送时间:2025-01-06 22:12:15 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Freesurfer Digest, Vol 251, Issue 6
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://secure-web.cisco.com/19u5yrx1hEBh57aEQRnpFtUiQK-dS5rJ76xYC65HhTa_BvN... or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: [ext] Re: Freeview crash (Tietze, Anna)
- How to Plot Surface with ROI Boundaries Using Harvard-Oxford Brain Atlas? (Zeng, Xinglin)
- Re: [ext] Re: Freeview crash (Wang, Ruopeng)
- Re: [ext] Re: Freeview crash (Dicamillo, Robert)
- registration error (Ramesh Babu)
- Re: [External] Re: Assistance with mri_vol2surf: Missing Surface Values in Output (Douglas N. Greve)
Message: 1 Date: Fri, 3 Jan 2025 20:58:14 +0000 From: "Tietze, Anna" anna.tietze@charite.de Subject: Re: [Freesurfer] [ext] Re: Freeview crash To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: 89FA2C60-63FF-4959-8039-0724E56EF3CC@charite.de Content-Type: text/plain; charset="utf-8"
External Email - Use CautionHi 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 CautionYes, 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://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4...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
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://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4...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
<smime.p7s> External Email - Use Caution External Email - Use Caution
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4... 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://secure-web.cisco.com/1C3Rm_EJQFroDFSeUXGwlWJGelS12bb9i0uJ0bBhV30bmwP... <https://secure-web.cisco.com/1C3Rm_EJQFroDFSeUXGwlWJGelS12bb9i0uJ0bBhV30bmwP... EvnvCxt9TqD/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . 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.
External Email - Use Caution
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1hhsmBghDvdXvV8bIdu3XWLPammaCaGvm3GPUp7fLDRWRr4...