Re: [Freesurfer] can´t open an image in Freeview {Disarmed}
External Email - Use Caution Hello Adam, I’m doing some work with a VirtualBox VM running Ubuntu 18.04 -but hosted from Mac OS instead of Windows. I will install the 6.0.0 freesurfer release in the Ubuntu VM and run some of the freeview command tests we use, but so far I have not seen the graphics behavior you describe. The VirtualBox software has some guest extensions to install in the Ubuntu OS that can help with performance and graphics. On the Mac I have seen that w/o additions like that installed, the entire VM window will flicker. I might also be able to try the Ubuntu VM on a Windows 10 machine. - R. On Oct 24, 2019, at 15:27, Adam Rytina adam.ryt...@outlook.cz wrote:External Email - Use CautionHello,Yes sure, I checked my setup of Freesurfer enviroment - the same as the wiki page I guess.I loaded an image from the freesurfer distribution directly from the command line - the same problem (the grey windows popping out).The strange thing is I´m running also FSL on Ubuntu VM without any problem, thereby I don´t think the issue is related to the Ubuntu VM. Moreover, I succesfully opened some images few days ago and the program was running without any problem. However, it took just a while and then this issued appeared again. There is just a grey window popping out (choosing all options run very quickly without any problem).Well, I´m totally helpless. I tried to download it again, run Freesurfer on Ubuntu 16. and 18. version but the problem still persists.RegardsAdamOd:fsbuild fsbu...@contbay.comOdesláno:středa 23. října 2019 7:30Komu:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduKopie:adam.ryt...@outlook.czadam.ryt...@outlook.czPředmět:Re: [Freesurfer] can´t open an image in FreeviewHello Adam,It’s not clear to me that the vtk libs are the issue.Please check that you setup your FREESURFER environment as listed on the freesurfer help/wiki pages,https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallIt looks like you would do (using sh or bash),$ export FREESURFER_HOME=/usr/local/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output showing your settings ..You could try loadingto see if the graphics look any different.$ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgzThe grey boxes could be from the VM not having enough CPU or video memory resources allocated to it and so the graphics refresh is slow. You could try running some other graphics applications in the VM to see if you get the same greyed out effect.If you run freeview from the command line with no args,$ freeview- then you should get an empty window with just some icons at the top. Is it sluggish trying to drag around the empty freesurfer window? If so, I would ask whoever setup the VM to try and improve its performance.You could also try setting this on the command line for the vtk libs - but it may not fix the graphics getting greyed out.$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FREESURFER_HOME/lib/vtk/lib/vtk5.6- R.On Oct 22, 2019, at 14:46, Adam Rytina adam.ryt...@outlook.cz wrote:External Email - Use CautionHello,thanks for your answer. Please see attached the screenshot.I typed "$ which freeview.bin" -- the output: "/usr/local/freesurfer/bin/freeview.bin"I typed "$ ldd `which freeview.bin` | grep not" -- the output: 20 files "libvtk...so.5.6 are not found" Please see the attached screenshot.While trying to install the packages (eg. "sudo apt-get install libvtkverdict.so.5.6"), the output is:Reading package lists... DoneBuilding dependency treeReading state information DoneE: Unable to locate package libvtkverdict..so.5.6E: Couldn't find any package by glob 'libvtkverdict.so.5.6'E: Couldn't find any package by regex 'libvtkverdict.so.5.6'What´s wrong? Please, could you advise me? I tried to run freeview on Ubuntu 16.04 and 18.04 as well but the problem still remains the same.Thanks a lot for your helpRegardsAdamOd:fsbuild fsbu...@contbay.comOdesláno:pondělí 21. října 2019 4:28Komu:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduKopie:adam.ryt...@outlook.czadam.ryt...@outlook.czPředmět:Re: [Freesurfer] can´t open an image in FreeviewHello Adam,Please check if you have a “freeview.bin” program.$ which freeview.binIf you get a path back with freeview.bin in it, e.g. something like/usr/local/freesurfer/bin/freeview.bin- then try the ldd command on freeview.bin,$ ldd `which freeview.bin` | grep not- then see if it lists that something is not found.- R.On Oct 19, 2019, at 03:27, Adam Rytina adam.ryt...@outlook.cz wrote:External Email - Use CautionHello,I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is?What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official
Re: [Freesurfer] can´t open an image in Freeview {Disarmed}
External Email - Use Caution Hello, Yes sure, I checked my setup of Freesurfer enviroment - the same as the wiki page I guess. I loaded an image from the freesurfer distribution directly from the command line - the same problem (the grey windows popping out). The strange thing is I´m running also FSL on Ubuntu VM without any problem, thereby I don´t think the issue is related to the Ubuntu VM. Moreover, I succesfully opened some images few days ago and the program was running without any problem. However, it took just a while and then this issued appeared again. There is just a grey window popping out (choosing all options run very quickly without any problem). Well, I´m totally helpless. I tried to download it again, run Freesurfer on Ubuntu 16. and 18. version but the problem still persists. Regards Adam Od: fsbuild Odesláno: středa 23. října 2019 7:30 Komu: freesurfer@nmr.mgh.harvard.edu Kopie: adam.ryt...@outlook.cz Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam, It’s not clear to me that the vtk libs are the issue. Please check that you setup your FREESURFER environment as listed on the freesurfer help/wiki pages, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall It looks like you would do (using sh or bash), $ export FREESURFER_HOME=/usr/local/freesurfer $ source $FREESURFER_HOME/SetUpFreeSurfer.sh … output showing your settings ... .. . You could try loading to see if the graphics look any different. $ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgz The grey boxes could be from the VM not having enough CPU or video memory resources allocated to it and so the graphics refresh is slow. You could try running some other graphics applications in the VM to see if you get the same greyed out effect. If you run freeview from the command line with no args, $ freeview - then you should get an empty window with just some icons at the top. Is it sluggish trying to drag around the empty freesurfer window? If so, I would ask whoever setup the VM to try and improve its performance. You could also try setting this on the command line for the vtk libs - but it may not fix the graphics getting greyed out. $ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FREESURFER_HOME/lib/vtk/lib/vtk5.6 - R. On Oct 22, 2019, at 14:46, Adam Rytina wrote: External Email - Use Caution Hello, thanks for your answer. Please see attached the screenshot. I typed "$ which freeview.bin" --> the output: "/usr/local/freesurfer/bin/freeview.bin" I typed "$ ldd `which freeview.bin` | grep not" --> the output: 20 files "libvtk...so.5.6 are not found" Please see the attached screenshot. While trying to install the packages (eg. "sudo apt-get install libvtkverdict.so.5.6"), the output is: Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libvtkverdict..so.5.6 E: Couldn't find any package by glob 'libvtkverdict.so.5.6' E: Couldn't find any package by regex 'libvtkverdict.so.5.6' What´s wrong? Please, could you advise me? I tried to run freeview on Ubuntu 16.04 and 18.04 as well but the problem still remains the same. Thanks a lot for your help Regards Adam Od: fsbuild mailto:fsbu...@contbay.com>> Odesláno: pondělí 21. října 2019 4:28 Komu: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Kopie: adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz> mailto:adam.ryt...@outlook.cz>> Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam, Please check if you have a “freeview.bin” program. $ which freeview.bin If you get a path back with freeview.bin in it, e.g. something like /usr/local/freesurfer/bin/freeview.bin - then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep not - then see if it lists that something is not found. - R. On Oct 19, 2019, at 03:27, Adam Rytina mailto:adam.ryt...@outlook.cz>> wrote: External Email - Use Caution Hello, I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is? What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please, could you help me? Thanks a lot Adam Od: fsbuild mailto:fsbu...@contbay.com>> Odesláno: pátek 18.. října 2019 22:05 Komu: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Kopie: adam.ryt...@outlook.cz<mailto:adam.ryt..
Re: [Freesurfer] can´t open an image in Freeview {Disarmed}
External Email - Use Caution Hello Adam, It’s not clear to me that the vtk libs are the issue. Please check that you setup your FREESURFER environment as listed on the freesurfer help/wiki pages,https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall It looks like you would do (using sh or bash), $ export FREESURFER_HOME=/usr/local/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh… output showing your settings .. You could try loading an image from the freesurfer distribution directly from the command line to see if the graphics look any different. $ freeview $FRESURFER_HOME/subjects/bert/mri/brain.mgz The grey boxes could be from the VM not having enough CPU or video memory resources allocated to it and so the graphics refresh is slow. You could try running some other graphics applications in the VM to see if you get the same greyed out effect. If you run freeview from the command line with no args,$ freeview - then you should get an empty window with just some icons at the top. Is it sluggish trying to drag around the empty freesurfer window? If so, I would ask whoever setup the VM to try and improve its performance. You could also try setting this on the command line for the vtk libs - but it may not fix the graphics getting greyed out.$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FREESURFER_HOME/lib/vtk/lib/vtk5.6 - R. On Oct 22, 2019, at 14:46, Adam Rytina adam.ryt...@outlook.cz wrote:External Email - Use CautionHello,thanks for your answer. Please see attached the screenshot.I typed "$ which freeview.bin" -- the output: "/usr/local/freesurfer/bin/freeview.bin"I typed "$ ldd `which freeview..bin` | grep not" -- the output: 20 files "libvtk...so.5.6 are not found" Please see the attached screenshot.While trying to install the packages (eg. "sudo apt-get install libvtkverdict.so.5.6"), the output is:Reading package lists... DoneBuilding dependency treeReading state information... DoneE: Unable to locate package libvtkverdict.so.5.6E: Couldn't find any package by glob 'libvtkverdict.so.5.6'E: Couldn't find any package by regex 'libvtkverdict.so.5.6'What´s wrong? Please, could you advise me? I tried to run freeview on Ubuntu 16.04 and 18.04 as well but the problem still remains the same.Thanks a lot for your helpRegardsAdamOd:fsbuild fsbu...@contbay.comOdesláno:pondělí 21. října 2019 4:28Komu:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduKopie:adam.ryt...@outlook.czadam.ryt...@outlook.czPředmět:Re: [Freesurfer] can´t open an image in FreeviewHello Adam,Please check if you have a “freeview.bin” program.$ which freeview.binIf you get a path back with freeview.bin in it, e.g. something like/usr/local/freesurfer/bin/freeview.bin- then try the ldd command on freeview.bin,$ ldd `which freeview.bin` | grep not- then see if it lists that something is not found.- R.On Oct 19, 2019, at 03:27, Adam Rytina adam.ryt...@outlook.cz wrote:External Email - Use CautionHello,I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is?What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallPlease, could you help me?Thanks a lotAdamOd:fsbuild fsbu...@contbay.comOdesláno:pátek 18.. října 2019 22:05Komu:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduKopie:adam.ryt...@outlook.czadam.ryt...@outlook.czPředmět:Re: [Freesurfer] can´t open an image in FreeviewHello Adam,See if you can run the following command, and if it reports anything is not found (you can cut and paste the command)- R.$ ldd `which freeview` | grep notAdam RytinaOctober 18, 2019 at 14:31External Email - Use CautionHello all,I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6..0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue?Thanks a lotAdamBez virů.www.avast.com___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer___Freesurfer mailing listfreesur...@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferfreeview.png___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___
Re: [Freesurfer] can´t open an image in Freeview
External Email - Use Caution Hello, thanks for your answer. Please see attached the screenshot. I typed "$ which freeview.bin" --> the output: "/usr/local/freesurfer/bin/freeview.bin" I typed "$ ldd `which freeview.bin` | grep not" --> the output: 20 files "libvtk...so.5.6 are not found" Please see the attached screenshot. While trying to install the packages (eg. "sudo apt-get install libvtkverdict.so.5.6"), the output is: Reading package lists... Done Building dependency tree Reading state information... Done E: Unable to locate package libvtkverdict.so.5.6 E: Couldn't find any package by glob 'libvtkverdict.so.5.6' E: Couldn't find any package by regex 'libvtkverdict.so.5.6' What´s wrong? Please, could you advise me? I tried to run freeview on Ubuntu 16.04 and 18.04 as well but the problem still remains the same. Thanks a lot for your help Regards Adam Od: fsbuild Odesláno: pondělí 21. října 2019 4:28 Komu: freesurfer@nmr.mgh.harvard.edu Kopie: adam.ryt...@outlook.cz Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam, Please check if you have a “freeview.bin” program. $ which freeview.bin If you get a path back with freeview.bin in it, e.g. something like /usr/local/freesurfer/bin/freeview.bin - then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep not - then see if it lists that something is not found. - R. On Oct 19, 2019, at 03:27, Adam Rytina wrote: External Email - Use Caution Hello, I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is? What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please, could you help me? Thanks a lot Adam Od: fsbuild mailto:fsbu...@contbay.com>> Odesláno: pátek 18.. října 2019 22:05 Komu: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> mailto:freesurfer@nmr.mgh.harvard.edu>> Kopie: adam.ryt...@outlook.cz<mailto:adam.ryt...@outlook.cz> mailto:adam.ryt...@outlook.cz>> Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam, See if you can run the following command, and if it reports anything is not found (you can cut and paste the command) - R. $ ldd `which freeview` | grep not Adam Rytina<mailto:adam.ryt...@outlook.cz> October 18, 2019 at 14:31 External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> Bez virů. www.avast.com<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list freesur...@nmr.mgh..harvard.edu https://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
Re: [Freesurfer] can´t open an image in Freeview
External Email - Use Caution Hello Adam, Please check if you have a “freeview.bin” program. $ which freeview.bin If you get a path back with freeview.bin in it, e.g. something like/usr/local/freesurfer/bin/freeview.bin - then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep not - then see if it lists that something is not found. - R. On Oct 19, 2019, at 03:27, Adam Rytina adam.ryt...@outlook.cz wrote:External Email - Use CautionHello,I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is?What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallPlease, could you help me?Thanks a lotAdamOd:fsbuild fsbu...@contbay.comOdesláno:pátek 18. října 2019 22:05Komu:freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.eduKopie:adam.ryt...@outlook.czadam.ryt...@outlook.czPředmět:Re: [Freesurfer] can´t open an image in FreeviewHello Adam,See if you can run the following command, and if it reports anything is not found (you can cut and paste the command)- R.$ ldd `which freeview` | grep notAdam RytinaOctober 18, 2019 at 14:31External Email - Use CautionHello all,I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue?Thanks a lotAdamBez virů.www.avast.com___Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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
Re: [Freesurfer] can´t open an image in Freeview
External Email - Use Caution Hello, I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is? What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please, could you help me? Thanks a lot Adam Od: fsbuild Odesláno: pátek 18. října 2019 22:05 Komu: freesurfer@nmr.mgh.harvard.edu Kopie: adam.ryt...@outlook.cz Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam, See if you can run the following command, and if it reports anything is not found (you can cut and paste the command) - R. $ ldd `which freeview` | grep not Adam Rytina<mailto:adam.ryt...@outlook.cz> October 18, 2019 at 14:31 External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam [https://ipmcdn.avast.com/images/icons/icon-envelope-tick-round-orange-animated-no-repeat-v1.gif]<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> Bez virů. www.avast.com<https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
Re: [Freesurfer] can´t open an image in Freeview
External Email - Use Caution Hello Adam, See if you can run the following command, and if it reports anything is not found (you can cut and paste the command) - R. $ ldd `which freeview` | grep not Adam RytinaOctober 18, 2019 at 14:31 External Email - Use Caution Hello all, I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue? Thanks a lot Adam Bez virů. www.avast.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
