External Email - Use Caution
I should add: I've used this license file for several years wtih FS v.5.1, v5.3, v6, v7+ and developer versions. It runs FreeSurfer perfectly on two MacOS computers and on a RedHat Linux cluster where it has run thousands of recons + additional processing.
The license file continued to work -- I could run FreeSurfer commands with it and it never reported a missing or unreadable license file.
So if you are getting segfaults and you think you have a good license -- try requesting a new one just in case.
On Mon, Aug 2, 2021 at 10:10 AM Adam Martersteck acmarter@gmail.com wrote:
Confirm, just requesting a new license file fixed my FreeView MacOS 11.4 segfault errors.
Requesting a new license file with my same credentials produced an identical text file (same email, same license #, same two strings of random letter/digit/symbols).
*I didn't even need to download the new license file* (as the identical one was already present) or move it into the /Applications/freesurfer/7.2.0 directory -- FreeView just began to work perfectly fine with my previously present license.
This fixed my unusable FreeView in /Applications/freesurfer/7.1.1/ also. Same license file was present there, never needed to download the newly requested one. Just the *act of requesting a new license file fixed it*.
Strange, right? Doesn't sound like a Mac OS permission problem, sounds like an issue with my license registration?
On Mon, Aug 2, 2021 at 4:41 AM fsbuild fsbuild@contbay.com wrote:
External Email - Use CautionAfter some feedback and some more testing, I can reproduce that freeview.app in the 7.2.0 release will segfault on MacOS 11.4 if the license file cannot be found or it cannot be read. One user reported that he had to get a new license file in order for it to work. The link for that is here, https://secure-web.cisco.com/1ET788Mna2WVAEWKpm4YiU1xXU3qn8bJGFhxXkO9s6jJXdt...
- R..
On Jul 29, 2021, at 14:34, Adam Martersteck acmarter@gmail.com wrote:
External Email - Use CautionHere'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!
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