External Email - Use Caution        

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 <fsbu...@contbay.com> wrote:

>         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/102goTLYZghbG1one7hITbEMVONyU-O0jWQPIskDdkuDmhaxukoGaD5jlQDVIL4CtgvPnUVDXBXw9XKnoFnMInD9ikZqA2brbFYnISp85z7Hc9trSiRbOP4QaFGptReMLpFauRZaqFaFbqFoDVkvD1kx1BZxSteV2e5Q6jrFPf-YEcIImmcloqwIqP8Lh2lnSy5aLFUp8K9mERr6dYmb0OhnvW_rEkD7__biFcC5PAxgQXOLA-8GdeO0SES2PBZDvT6wg4_mvqRFFPHORULo23A/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=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 <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
>> $ 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 <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 list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>
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> <freeview_QT_DEBUG_log.txt>_______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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