External Email - Use Caution
After 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/1wLe38Ld2-MJosql9_igECcekBov1nUay8lBJ4gNTyOy7CMKYpu0qhOebXHKkjJcq50BBjrmG1r0LVvavWylVU7gtzxzH-H0TwRBJnWZtIxnTEp0PXkzqmAryNMlqopJhQ96A5QROiaGzPNVj1lIMcieRGjjyt9xhXMEH7GTbJnvCpxNV2Ncf0mSHHUiMPyznxSP0HYeUw9xpwrQsquBDiHr3zkgVMVc-gBH5_RLzCTQCSS7mnT6tOetgNsfkZiN32shJYQrHz9fEuTFD4fSosg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
- R.
On Jul 29, 2021, at 14:34, Adam Martersteck <acmar...@gmail.com>
wrote: 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=1I 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.-AdamOn Wed, Jul 28,
2021 at 8:53 PM fsbuild <fsbu...@contbay.com>
wrote: External Email - Use
Caution 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$
bash2) setup freesurfer environment$ export
FREESURFER_HOME=/Applications/freesurfer/7.2.0$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh--------
freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b --------Setting up environment
for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME
/Applications/freesurfer/7.2.0FSFAST_HOME
/Applications/freesurfer/7.2.0/fsfastFSF_OUTPUT_FORMAT
nii.gzSUBJECTS_DIR
/Applications/freesurfer/7.2.0/subjectsMNI_DIR
/Applications/freesurfer/7.2.0/mni3) Locate your license file (I name mine
license.txt) in your home directory and check you can read its contents,$
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=15) 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 <fsbu...@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.br...@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
<tomparke...@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
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behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<freeview_QT_DEBUG_log.txt>_______________________________________________Freesurfer
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