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If you have not already done so, see if you get a different result by double clicking on the Freeview.app icon under /Applications/freesurfer/7.2.0 with the mouse.
You can try this variation on what's been previously suggested.
1) run a bash shell $ bash
2) setup freesurfer environment $ export FREESURFER_HOME=/Applications/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.2.0 FSFAST_HOME /Applications/freesurfer/7..2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects MNI_DIR /Applications/freesurfer/7.2.0/mni
3) Locate your license file (I name mine license.txt) in your home directory and check you can read its contents, $ export FS_LICENSE=$HOME/license.txt $ cat $FS_LICENSE .... check the output ... .... first line should contain email address ... .... followed by 3 more lines ...
4) set environment variable for debug $ export QT_DEBUG_PLUGINS=1
5) run freeview with no arguments $ which freeview /Applications/freesurfer/7.2.0/bin/freeview $ freeview
.... an empty freeview window should appear and persist on the screen ...
At this point the last few lines of output in the terminal window should now be:
Got keys from plugin meta data ("svg", "svgz", "svg.gz") QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/iconengines" ... QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/accessible" ... QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/accessible" ...
6) Use the freeview application "File" pull down menu to select "load volume". In the window that comes up, click on the yellow folder icon to the r.h.s of the folder/file entry box under "Select Volume File". In the Finder window that comes up, navigate to /Applications/freesurfer/7.2.0/subjects/bert/mri and select the brain.mgz file. Click on OPEN. That path/filename will appear in the load volume text entry box. Don't check/change any of the options for loading the volume and click OK.
The steps above worked for me to load that volume using an Intel MacPro laptop with the 7.2.0 release running under either MacOS 10.15.7 (Catlaina) or MacOS 11.4 (Big Sur) w/o freeview exiting or producing any further output in the terminal window. If it fails on your machine, you could send along the Qt debug output after the lines listed above. Please do not send the output from cat'ing your license file though.
- R.On Jul 28, 2021, at 14:53, fsbuild <fsbuild@contbay.com> wrote: External Email - Use Caution Please check in “energy saver” preferences that “automatic graphics switching” is not selected so that high performance graphics is always used.- R.On Jul 28, 2021, at 14:36, Sahil Bajaj <sahil.brain@gmail.com> wrote: External Email - Use Caution Hi Freesurfer team,I am also having a similar issue from the last few weeks. I hope we will get a solution soon.Thanks,Sahil On Wed, Jul 28, 2021 at 11:15 AM Tom Parker <tomparker59@gmail.com> wrote: External Email - Use Caution I have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below.Any advice to correct would be much appreciated.Many thanks!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer________________... mailing listFreesurfer@nmr.mgh.harvard.eduMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-UOGTt3HFDlHvIM_e7oJsIyW0px6D2XV4xw3FKWnt4xh3s... mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Here's a log from a completely clean install of FreeSurfer 7.2.0.
On an Intel processor MacBook Pro, running macOS Big Sur (11.4).
__Starting with a completely clean install of FreeSurfer 7.2.0__ Copied license file over from 7.1.1. (Confirmed license file works by running mri_convert)
MacBook-Pro:freesurfer adam$ freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38945 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" MacBook-Pro:freesurfer adam$ freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38951 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" MacBook-Pro:freesurfer adam$ freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38954 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" MacBook-Pro:freesurfer adam$ freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38974 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" MacBook-Pro:freesurfer adam$ freeview /Applications/freesurfer/7.2.0/bin/freeview: line 2: 38977 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@"
(Line numbers that it faults at are linearly increasing?)
With export QT_DEBUG_PLUGINS=1
I have attached the output log from "freeview > freeview_QT_DEBUG_log.txt". The tail of it is: " loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqtiff.dylib" loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwbmp.dylib" loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib" /Applications/freesurfer/7.2.0/bin/freeview: line 2: 39147 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" "
It perfectly replicates in FreeSurfer 7.1.1. Same error, same debug log.
-Adam
On Wed, Jul 28, 2021 at 8:53 PM fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionIf you have not already done so, see if you get a different result by double clicking on the Freeview.app icon under /Applications/freesurfer/7.2.0 with the mouse.
You can try this variation on what's been previously suggested.
- run a bash shell
$ bash
- setup freesurfer environment
$ export FREESURFER_HOME=/Applications/freesurfer/7.2.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.2.0 FSFAST_HOME /Applications/freesurfer/7.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.2.0/subjects MNI_DIR /Applications/freesurfer/7.2.0/mni
- Locate your license file (I name mine license.txt) in your home
directory and check you can read its contents, $ export FS_LICENSE=$HOME/license.txt $ cat $FS_LICENSE ... check the output ... ... first line should contain email address ... ... followed by 3 more lines ...
- set environment variable for debug
$ export QT_DEBUG_PLUGINS=1
- run freeview with no arguments
$ which freeview /Applications/freesurfer/7.2.0/bin/freeview $ freeview
... an empty freeview window should appear and persist on the screen ...
At this point the last few lines of output in the terminal window should now be:
Got keys from plugin meta data ("svg", "svgz", "svg.gz") QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/iconengines" ... QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/accessible" ... QFactoryLoader::QFactoryLoader() checking directory path "/Applications/freesurfer/7.2.0/Freeview.app/Contents/MacOS/accessible" ...
- Use the freeview application "File" pull down menu to select "load
volume". In the window that comes up, click on the yellow folder icon to the r.h.s of the folder/file entry box under "Select Volume File". In the Finder window that comes up, navigate to /Applications/freesurfer/7.2.0/subjects/bert/mri and select the brain.mgz file.. Click on OPEN. That path/filename will appear in the load volume text entry box. Don't check/change any of the options for loading the volume and click OK.
The steps above worked for me to load that volume using an Intel MacPro laptop with the 7.2.0 release running under either MacOS 10.15.7 (Catlaina) or MacOS 11.4 (Big Sur) w/o freeview exiting or producing any further output in the terminal window. If it fails on your machine, you could send along the Qt debug output after the lines listed above. Please do not send the output from cat'ing your license file though.
- R.
On Jul 28, 2021, at 14:53, fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionPlease check in “energy saver” preferences that “automatic graphics switching” is not selected so that high performance graphics is always used.
- R.
On Jul 28, 2021, at 14:36, Sahil Bajaj sahil.brain@gmail.com wrote:
External Email - Use CautionHi Freesurfer team,
I am also having a similar issue from the last few weeks. I hope we will get a solution soon.
Thanks, Sahil
On Wed, Jul 28, 2021 at 11:15 AM Tom Parker tomparker59@gmail.com wrote:
External Email - Use CautionI have just installed Freesurfer 7.2.0 for Mac. When I attempt to open Freeview it crashes. Full details of error messages below.
Any advice to correct would be much appreciated.
Many thanks!
Freesurfer mailing list 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/1Kedvuo4iWeliWYz243T7FMJA3mrmnb_6kGyoerF8tSq8SB... https://secure-web.cisco.com/1t1kuIF7XgQYTpBRMwhddkd-yOxfUwwwvnaK_M_D_bGquaLgl2i1hE9k6Xkv3DEawq9f4KUm6g4F6zzMrRT8pK2X6E4VdvUmrnVH6atV2_9bJGjVAnjPCMwTdUdwalVncBCiLxXVUSeU8cI7JM8cDrLtmXlj7gCcQM210FcX7Q6PMELupUfyBMr1zjmt_CKh-OOHsu4NVifIBWr812nQVqfwiWX-eTRWggOVMfEyAkhJ_r0zH_L1EUlW4fGVADHFMrHRcJQp5WzKgs6Y7-9o0Aw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list 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/1Kedvuo4iWeliWYz243T7FMJA3mrmnb_6kGyoerF8tSq8SB... https://secure-web.cisco.com/1QLw3KeluW_bEzIDPhPT9faqoleG2__3MCagK-6vum3UeQJ9qPUFYrvOFahJXyvwKKHRj68h1TtDRztMfQXV75vgJKxR-1kNXo2mRseNbcyjX2l3U8eLawMfbDfXgSEHjtkh-gmeFhco9O4rM9Q48hKOzqkfgxFG8OWyEAQGIXiw71PYK4Enf0oWaWlF4LQZ70yLKPaJaLV8FfEfj8GymyapIVFWRJKDmY9t8BPOUQ4ZaZOxpqMm_JN8PRpnFOjHSQq1WxYI7DaV3MCn6KVlL3A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Kedvuo4iWeliWYz243T7FMJA3mrmnb_6kGyoerF8tSq8SB...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Kedvuo4iWeliWYz243T7FMJA3mrmnb_6kGyoerF8tSq8SB...
freesurfer@nmr.mgh.harvard.edu
-
Adam Martersteck -
fsbuild