Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
External Email - Use Caution Sure thing. I'm not sure if my last email was sent as it contained images > listserv allowable size, so I've reposted it here, hosting the images on imgur. I've tested it on 4 monitors, all at 2560x1440p native resolutions. An ASUS PB278, an ASUS ROG PG278Q, a GIGABYTE M27Q, an an ACER XV272U. Here are the mac display preferences testing each individually: https://secure-web.cisco.com/16lOiIxQERu3wh-MTKeMFlvUWq-wGbKK7Og-Z9-0MVKa9UwQCDVwTeKHc--TAn3cWFYyiV0PM33EbLnEjkBbhEdDxMb-JK6jmF62tTKgJLS4hJ3jdW2ps1Z1ZELCuT6fZr1DRFkwT-mI0q8R4SXUsRLvuzHU0fKhjdzvDgn227HnFa91fa9_yMIZmz_J7anB5tmP90ta9lKOrJBZz2xIGjPgxfPy574gtgwt2Gid4KxuMg0j458uUjEsJbzYpOfUfoUBzgMg16HqEla_8yEh0PA/https%3A%2F%2Fimgur.com%2Fa%2FAcryUsH I tested with and without "Default for display" and "Scaled". Each time the monitor was set to "Default for display" or scaled to 2560x1440p or scaled to any resolution > 1600x900, FreeView seg faults at: " loaded library "/Applications/freesurfer/7.2.0/Freeview.app/Contents/PlugIns/imageformats/libqwebp.dylib" /Applications/freesurfer/7.2.0/bin/freeview: line 2: $NUMBER Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" " Not that I think it would make a difference, but for completeness, I also tested jittering the refresh rate between 30 and 144Hz, and tested with a USB-C-to-USB-C, displayport-to-USB-C, and HDMI-to-USB-C. Neither the adapter nor the refresh rate made a difference in behavior. On Mon, Aug 2, 2021 at 3:08 PM fsbuild wrote: > Thanks Adam for pointing out different behavior at different screen > resolutions. I would be interested to know if those resolutions are not > the native resolution of the external monitor. The manual/info for any > monitor should state what it’s native resolution is, e.g., for a 4K monitor > native resolution is 3840 X 2160. If you don’t have the displays > mirrored, I think when you select System Preferences -> Displays a window > will appear on each monitor. Under the Display tab try checking the box > "default for display" for any external monitor and not the "scale" option > for the hardware to scale the image up/down in size. > > - R. > > On Aug 2, 2021, at 16:08, Adam Martersteck wrote: > > 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 > 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 >> 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 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
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
External Email - Use Caution Thanks Adam for pointing out different behavior at different screen resolutions. I would be interested to know if those resolutions are not the native resolution of the external monitor. The manual/info for any monitor should state what it’s native resolution is, e.g.., for a 4K monitor native resolution is 3840 X 2160. If you don’t have the displays mirrored, I think when you select System Preferences - Displays a window will appear on each monitor. Under the Display tab try checking the box "default for display" for any external monitor and not the "scale" option for the hardware to scale the image up/down in size. - R. On Aug 2, 2021, at 16:08, Adam Martersteck acmar...@gmail.com wrote:External Email - Use CautionI started getting segfaults again but I was able to diagnose what was different.It turns out it wasnotthe 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 shouldadd: 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 withit 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 theact 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 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, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://secure-web.cisco.com/1MxE6xP8mPPjlSA8T50wRDKo-y1FrIDbXFfaR9j9rYsiDd2ZuhUnpj78tw1LE0aQ5KEdn5AjnbGLpd_g-xVUoDJndZrvyhsPzbUyhaOoIelzpXTsgCOmo8QrC62AwL-vzL2VmszuwyqzpSBxwGInwVGLdejf4yzQWB4m0_a2Kw2a3Iq-vjAIsGsnTbnOUF9LhLTL8YJYl1fFDwgs_hsspdzgqT3xO9iAbZqYlzwcsFlDNAeoDpP3spfJ0VUATy4K07j18TOGCn4uM4B5P0lsWyQ/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 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
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
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 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 > 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 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 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
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
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 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 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/1ET788Mna2WVAEWKpm4YiU1xXU3qn8bJGFhxXkO9s6jJXdtKLbhrUhl8OTrwNFjiqhXcjsJb86Yz-6R-DTgfHSEAzWDL0QgznDOjerB7-xv-KJYP9ECT_vGza0i7LICmv8c0YsLHQn7E8y2Bl3u8WH2t_ntW9Bbu7Zowx9ubjV4nrif-rv2oBgs3t4dO1En3qw4YxfrHuldvBQUvKX32TAyKrafsDcqI42e4hmx1fb3P-FTEwsLgeSqUyPcDTSVwcYI51XgdwgrICJqOfSNQtzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html >> >> - R.. >> >> On Jul 29, 2021, at 14:34, Adam Martersteck 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 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 >>> >>>
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
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 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 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 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 $FS_LICENSE >> ... check the output ... >> ... first line should contain email address ... >> ... followed by 3 more lines ... >> >> 4) set environment
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
External Email - Use Caution
After some feedback and some more testing, I can reproduce that freeview..app
in the 7.2.0 release will segfault on MacOS 11.4 if the license file cannot be
found or it cannot be read. One user reported that he had to get a new
license file in order for it to work. The link for that is here,
https://secure-web.cisco.com/1wLe38Ld2-MJosql9_igECcekBov1nUay8lBJ4gNTyOy7CMKYpu0qhOebXHKkjJcq50BBjrmG1r0LVvavWylVU7gtzxzH-H0TwRBJnWZtIxnTEp0PXkzqmAryNMlqopJhQ96A5QROiaGzPNVj1lIMcieRGjjyt9xhXMEH7GTbJnvCpxNV2Ncf0mSHHUiMPyznxSP0HYeUw9xpwrQsquBDiHr3zkgVMVc-gBH5_RLzCTQCSS7mnT6tOetgNsfkZiN32shJYQrHz9fEuTFD4fSosg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
- R.
On Jul 29, 2021, at 14:34, Adam Martersteck acmar...@gmail.com
wrote:External Email - Use
CautionHere's a log from a
completely clean install of FreeSurfer 7.2.0..On an Intel processor MacBook
Pro, running macOS Big Sur (11.4).__Starting with a completely clean install of
FreeSurfer 7.2.0__Copied license file over from 7.1.1.(Confirmed license file
works by running mri_convert)MacBook-Pro:freesurfer adam$
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=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
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.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
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
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 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 wrote:
>
>
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
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
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.br...@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,SahilOn Wed, Jul 28, 2021 at 11:15 AM Tom Parker
tomparke...@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
listfreesur...@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___Freesurfer
mailing listfreesur...@nmr.mgh.harvard.eduMailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to
behttps://secure-web.cisco.com/1-UOGTt3HFDlHvIM_e7oJsIyW0px6D2XV4xw3FKWnt4xh3sIPHm6M_lLyntdYycNGQTRaQ-kXzRWk5eyRK_dFjf6pm4W_yfiqh4y25j_bqoVho_pKD7oNfU_wubLkJsFaUXINWJIJNxzC5hNHu4_Ev29IaouL-yoZwwz4X78ptc5D5BEvdSXOi7niVuylnViwh0CIxaClSSS4QOwfjYLVmT8e4PQznkuPB0HMzbAfYwgB_00-oGhvBfkY7obfPRaRo46YfDCbkvt_MhcPFdgu7A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer___Freesurfer
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listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Mac install of Freesurfer 7.2.0 - Freeview quitsunexpectedly
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 CautionHi Freesurfer team,I am also having a similar issue from the last few weeks. I hope we will get a solution soon.Thanks,SahilOn Wed, Jul 28, 2021 at 11:15 AM Tom Parker tomparke...@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 listfreesur...@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___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
