External Email - Use Caution I started getting segfaults again but I was able to diagnose what was different.
It turns out it was *not the license file for me*. I registered a new license file this morning --> it worked on my Mac and I assumed it was the new license; I went into the office --> plugged my MacBook into my external monitor --> segfaults. Having a display with resolution > 1600x900 caused segfaults. At both 2048x1152 or 2560x1440, I am able to 100% replicate segfault error. FreeView does not launch. When I downsample the monitor to 1600x900 or 720p or unplug the monitor, I can open FreeView without error. Hope this helps other people out there. My graphics card on the 13" MacBook Pro is the Intel Iris Plus Graphics (1536 MB) from the Quad-Core Intel i5. On Mon, Aug 2, 2021 at 10:28 AM Adam Martersteck <acmar...@gmail.com> wrote: > 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 <acmar...@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 <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/1JT3c7LfejGgdeFtwp5oXVewAdlgS-PXun8Ll2vrvO3YVB4MLUBp6y5E6-moEJz-n3__ZoHW9nv47Vz-rEnv3yCVZWjr06kLa-8j0W6M3By99rzKoyk0Z3mKWDuyucyiBcvV-UP4u4Iq9OoGR7kWUwvOKoY69EADHqSBQ2FIFoYRD--obaSUHHWuG9W-CmGbbInwqbrdVlIq1puTTtffxc-jSWIALoj2Lars9kYDqMEsHjFZcbYyYih8n6FF9WveXFQi_Zs9tYevF5KSNiYFm2g/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 >>>>> *MailScanner has detected a possible fraud attempt from >>>>> "secure-web.cisco.com" claiming to be* >>>>> https://secure-web.cisco.com/1_ot4JsW1jANUj4vId5JkeUfilzXQ6Rr3-8DVacct6YY7dU9qVtY7reCukm7niS7jJlGU5FJzXrjOmzyZSSYjrfhs46Ur12LefSHemYFaiEv6U-gg_bKbWNczwFPMzHd3sfyKqDyORgqtOvGOBm-qm95KRMpSTHnhUBbhh7CwjvpFMACi4WhJmcaZcDqg3Yjw1YK7StSkZKVj6o1ucQVys5EjWWPvoDxiLVY_vCh8DP1SbFNrAQrGAlcIhCl2rz9PAYBChvEn5QizWXyxZ76tpw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>>> <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/1_ot4JsW1jANUj4vId5JkeUfilzXQ6Rr3-8DVacct6YY7dU9qVtY7reCukm7niS7jJlGU5FJzXrjOmzyZSSYjrfhs46Ur12LefSHemYFaiEv6U-gg_bKbWNczwFPMzHd3sfyKqDyORgqtOvGOBm-qm95KRMpSTHnhUBbhh7CwjvpFMACi4WhJmcaZcDqg3Yjw1YK7StSkZKVj6o1ucQVys5EjWWPvoDxiLVY_vCh8DP1SbFNrAQrGAlcIhCl2rz9PAYBChvEn5QizWXyxZ76tpw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> <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 >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1_ot4JsW1jANUj4vId5JkeUfilzXQ6Rr3-8DVacct6YY7dU9qVtY7reCukm7niS7jJlGU5FJzXrjOmzyZSSYjrfhs46Ur12LefSHemYFaiEv6U-gg_bKbWNczwFPMzHd3sfyKqDyORgqtOvGOBm-qm95KRMpSTHnhUBbhh7CwjvpFMACi4WhJmcaZcDqg3Yjw1YK7StSkZKVj6o1ucQVys5EjWWPvoDxiLVY_vCh8DP1SbFNrAQrGAlcIhCl2rz9PAYBChvEn5QizWXyxZ76tpw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> <https://secure-web.cisco.com/1Kedvuo4iWeliWYz243T7FMJA3mrmnb_6kGyoerF8tSq8SB-pL2lNqd-fV1-75N9Vk9lSQi43c2x4EsfDduGo0JKzcexLldAiIKnwZsjrbqqfgTEiF-naStbWuLvUoGsxxg_9m3TiK0ynZzVkTwjbBbXUOcC3tcMix-v2ixKeen3jF8IlpL8wewdhZI3CdEaEP9OFG6g3rwLsUrOoD9nYxmIizHMeli-Yh-qi5WLnOURuKo8Ho9LB7FaFuQ4_B-NPuq-E5bfxNE8LJPZgY4zpWg/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/1_ot4JsW1jANUj4vId5JkeUfilzXQ6Rr3-8DVacct6YY7dU9qVtY7reCukm7niS7jJlGU5FJzXrjOmzyZSSYjrfhs46Ur12LefSHemYFaiEv6U-gg_bKbWNczwFPMzHd3sfyKqDyORgqtOvGOBm-qm95KRMpSTHnhUBbhh7CwjvpFMACi4WhJmcaZcDqg3Yjw1YK7StSkZKVj6o1ucQVys5EjWWPvoDxiLVY_vCh8DP1SbFNrAQrGAlcIhCl2rz9PAYBChvEn5QizWXyxZ76tpw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>>> <https://secure-web.cisco.com/1raESC1mWjjNJJcfvJRWM_b7Wmas4O-dJQFO3Fzt2eqbkmoA0t6tcqedFXJe-QTEdFxvYSOc6nZUeNE_W2eZxhXzfckOvXYQzAq5mylDaUP7U7ekUoWsjuxHQyq0BvES7Hxx76XCTLa1AxRvoYVAMD5BE14A-YGaVs9MZwbZ2TuSGUen0_H_AL1dvpdDh8LyyAgasjsfXaFmcyAtYxHynmhUT3lbaqFJk0FkQaE07qdsvxgc9BjEixfFxNRHltXI0EcZSLMLhcJaUsr6mnWOoLQ/https%3A%2F%2Fsecure-web.cisco..com%2F1Kedvuo4iWeliWYz243T7FMJA3mrmnb_6kGyoerF8tSq8SB-pL2lNqd-fV1-75N9Vk9lSQi43c2x4EsfDduGo0JKzcexLldAiIKnwZsjrbqqfgTEiF-naStbWuLvUoGsxxg_9m3TiK0ynZzVkTwjbBbXUOcC3tcMix-v2ixKeen3jF8IlpL8wewdhZI3CdEaEP9OFG6g3rwLsUrOoD9nYxmIizHMeli-Yh-qi5WLnOURuKo8Ho9LB7FaFuQ4_B-NPuq-E5bfxNE8LJPZgY4zpWg%2Fhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer> >>> >>> <freeview_QT_DEBUG_log.txt> >>> _______________________________________________ >>> 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/1_ot4JsW1jANUj4vId5JkeUfilzXQ6Rr3-8DVacct6YY7dU9qVtY7reCukm7niS7jJlGU5FJzXrjOmzyZSSYjrfhs46Ur12LefSHemYFaiEv6U-gg_bKbWNczwFPMzHd3sfyKqDyORgqtOvGOBm-qm95KRMpSTHnhUBbhh7CwjvpFMACi4WhJmcaZcDqg3Yjw1YK7StSkZKVj6o1ucQVys5EjWWPvoDxiLVY_vCh8DP1SbFNrAQrGAlcIhCl2rz9PAYBChvEn5QizWXyxZ76tpw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <https://secure-web.cisco.com/1_nuzaEPCTI87b7j_N9p0SOPU-l-ErJXYTKGSzE-FZutyRbPHWKWV7MJoAWE2eI_gd6ogqcuf5GnM13y2x48R_Y7ghuXKLrFOxWh-V0g2cS9-HpL6hW6PizNayXg5gEGnpgWU_NizPJZ8dBfPOtHmdvINaHG5JRkn6Tb7AQPSylWjSw1a4E_6j3GsbN-vzWUwqpY5hhuL4eMVa5YHpNra-dFKgd49WXSAHSJ0JDkjGynPMxB7IRXgl8w8X1dYIG3skgMxMEIqUHu8vTCfesYxkA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> >>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://secure-web.cisco.com/1_ot4JsW1jANUj4vId5JkeUfilzXQ6Rr3-8DVacct6YY7dU9qVtY7reCukm7niS7jJlGU5FJzXrjOmzyZSSYjrfhs46Ur12LefSHemYFaiEv6U-gg_bKbWNczwFPMzHd3sfyKqDyORgqtOvGOBm-qm95KRMpSTHnhUBbhh7CwjvpFMACi4WhJmcaZcDqg3Yjw1YK7StSkZKVj6o1ucQVys5EjWWPvoDxiLVY_vCh8DP1SbFNrAQrGAlcIhCl2rz9PAYBChvEn5QizWXyxZ76tpw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
