External Email - Use Caution
Dear Freesurfer community,
I have been also experiencing problem that freeview froze when I tried to select and open a new volume file. This started after I upgraded mac OS X to Catalina. Until that I have been using freeview fine for five years.
Error message said
Last login: Thu Jan 23 13:43:03 on ttys000 [tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer [tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl [tup09900bj11:~] tomotarui% freeview 2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
I do have read permissions for those volume files when I checked with ls -l and mri_info. I have tried cleaned up and reinstall freesurfer, which did not solve the problem. It may be unique to my computer, but I would appreciate very much for any recommendation. Tomo
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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail.
Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.
You probably need to grant freeview permission to access your files and folders if you have not. You can check in System Preferences.
Ruopeng
On 1/23/20 2:16 PM, Tarui, Tomo wrote:
External Email - Use Caution
Dear Freesurfer community,
I have been also experiencing problem that freeview froze when I tried to select and open a new volume file. This started after I upgraded mac OS X to Catalina. Until that I have been using freeview fine for five years.
Error message said
Last login: Thu Jan 23 13:43:03 on ttys000 [tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer [tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl [tup09900bj11:~] tomotarui% freeview 2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
I do have read permissions for those volume files when I checked with ls -l and mri_info. I have tried cleaned up and reinstall freesurfer, which did not solve the problem. It may be unique to my computer, but I would appreciate very much for any recommendation. Tomo
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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail.
Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thank you very much for your prompt advice. I have granted freeview the permission to access all files through System Preferences —> Security & Privacy —> Privacy (then restarted computer). Unfortunately, the freeview still freezes when attempting to open a new file. Following are additional lines of error messages. I would appreciate for your advice again.
[Tomo-no-iMac:~] tomotarui% freeview 2020-01-23 15:05:44.369 Freeview[876:10904] -_continuousScroll is deprecated for NSEventTypeScrollWheel. Please use -hasPreciseScrollingDeltas. 2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaX is deprecated for NSEventTypeScrollWheel. Please use -scrollingDeltaX. 2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaY is deprecated for NSEventTypeScrollWheel. Please use -scrollingDeltaX. 2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaZ is deprecated for NSEventTypeScrollWheel. Please use -scrollingDeltaX. 2020-01-23 15:05:50.197 Freeview[876:10904] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
** I force closed freeview here **
020-01-23 15:11:19.499 Freeview[876:10904] WARNING: <NSOpenPanel: 0x7f9ad6455330> found it necessary to prepare implicitly; please prepare panels using NSSavePanel rather than NSApplication or NSWindow. 2020-01-23 15:11:19.518 Freeview[876:10904] WARNING: <NSOpenPanel: 0x7f9ad6455330> found it necessary to start implicitly; please start panels using NSSavePanel rather than NSApplication or NSWindow. 2020-01-23 15:11:19.518 Freeview[876:10904] WARNING: <NSOpenPanel: 0x7f9ad6455330> running implicitly; please run panels using NSSavePanel rather than NSApplication. 2020-01-23 15:11:19.519 Freeview[876:10904] -[NSApplication runModalSession:]: Use of freed session detected. Do not call runModalSession: after calling endModalSesion:. 2020-01-23 15:11:19.548 Freeview[876:10904] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
Tomo
On Jan 23, 2020, at 14:21, Ruopeng Wang <rpwang@nmr.mgh.harvard.edumailto:rpwang@nmr.mgh.harvard.edu> wrote:
EXTERNAL MESSAGE - TREAT LINKS/FILES WITH CARE
You probably need to grant freeview permission to access your files and folders if you have not. You can check in System Preferences.
Ruopeng
On 1/23/20 2:16 PM, Tarui, Tomo wrote:
External Email - Use Caution
Dear Freesurfer community,
I have been also experiencing problem that freeview froze when I tried to select and open a new volume file. This started after I upgraded mac OS X to Catalina. Until that I have been using freeview fine for five years.
Error message said
Last login: Thu Jan 23 13:43:03 on ttys000 [tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer [tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl [tup09900bj11:~] tomotarui% freeview 2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
I do have read permissions for those volume files when I checked with ls -l and mri_info. I have tried cleaned up and reinstall freesurfer, which did not solve the problem. It may be unique to my computer, but I would appreciate very much for any recommendation. Tomo
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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail.
Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail.
Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.
You can try updating your version of freeview following the instructions at https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview. The freeview version shipped with FS 6.0 uses some pretty old Qt libraries, so upgrading might fix this… hopefully Andrew
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Tarui, Tomo" TTarui@tuftsmedicalcenter.org Reply-To: FS Help freesurfer@nmr.mgh.harvard.edu Date: Thursday, January 23, 2020 at 3:15 PM To: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [EXT] Re: Freeview froze when trying to open volume file
External Email - Use Caution Thank you very much for your prompt advice. I have granted freeview the permission to access all files through System Preferences —> Security & Privacy —> Privacy (then restarted computer). Unfortunately, the freeview still freezes when attempting to open a new file. Following are additional lines of error messages. I would appreciate for your advice again.
[Tomo-no-iMac:~] tomotarui% freeview 2020-01-23 15:05:44.369 Freeview[876:10904] -_continuousScroll is deprecated for NSEventTypeScrollWheel. Please use -hasPreciseScrollingDeltas. 2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaX is deprecated for NSEventTypeScrollWheel. Please use -scrollingDeltaX. 2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaY is deprecated for NSEventTypeScrollWheel. Please use -scrollingDeltaX. 2020-01-23 15:05:44.369 Freeview[876:10904] -deviceDeltaZ is deprecated for NSEventTypeScrollWheel. Please use -scrollingDeltaX. 2020-01-23 15:05:50.197 Freeview[876:10904] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
** I force closed freeview here **
020-01-23 15:11:19.499 Freeview[876:10904] WARNING: <NSOpenPanel: 0x7f9ad6455330> found it necessary to prepare implicitly; please prepare panels using NSSavePanel rather than NSApplication or NSWindow. 2020-01-23 15:11:19.518 Freeview[876:10904] WARNING: <NSOpenPanel: 0x7f9ad6455330> found it necessary to start implicitly; please start panels using NSSavePanel rather than NSApplication or NSWindow. 2020-01-23 15:11:19.518 Freeview[876:10904] WARNING: <NSOpenPanel: 0x7f9ad6455330> running implicitly; please run panels using NSSavePanel rather than NSApplication. 2020-01-23 15:11:19.519 Freeview[876:10904] -[NSApplication runModalSession:]: Use of freed session detected. Do not call runModalSession: after calling endModalSesion:. 2020-01-23 15:11:19.548 Freeview[876:10904] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
Tomo
On Jan 23, 2020, at 14:21, Ruopeng Wang <rpwang@nmr.mgh.harvard.edumailto:rpwang@nmr.mgh.harvard.edu> wrote:
EXTERNAL MESSAGE - TREAT LINKS/FILES WITH CARE You probably need to grant freeview permission to access your files and folders if you have not. You can check in System Preferences. Ruopeng On 1/23/20 2:16 PM, Tarui, Tomo wrote: External Email - Use Caution Dear Freesurfer community,
I have been also experiencing problem that freeview froze when I tried to select and open a new volume file. This started after I upgraded mac OS X to Catalina. Until that I have been using freeview fine for five years.
Error message said
Last login: Thu Jan 23 13:43:03 on ttys000 [tup09900bj11:~] tomotarui% setenv FREESURFER_HOME /Applications/freesurfer [tup09900bj11:~] tomotarui% source $FREESURFER_HOME/SetUpFreeSurfer.csh -------- freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl [tup09900bj11:~] tomotarui% freeview 2020-01-23 13:54:35.305 Freeview[3205:65482] modalSession has been exited prematurely - check for a reentrant call to endModalSession:
I do have read permissions for those volume files when I checked with ls -l and mri_info. I have tried cleaned up and reinstall freesurfer, which did not solve the problem. It may be unique to my computer, but I would appreciate very much for any recommendation. Tomo
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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail.
Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 Tufts Medical Center HIPAA Hotline at (617) 636-4422. If the e-mail was sent to you in error but does not contain patient information, contact the sender and properly dispose of the e-mail.
Please consider the environment and the security of the information contained within or attached to this e-mail before printing or saving to an insecure location.
freesurfer@nmr.mgh.harvard.edu
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Hoopes, Andrew -
Ruopeng Wang -
Tarui, Tomo