External Email - Use Caution In your terminal window after you’ve sourced the freesurfer setup script you should be able to do,$ which freeview … and it will show something like … /usr/local/freesurfer/bin/freeview So using whatever that absolute path is to freeview on your system, then do, $ ldd /usr/local/freesurfer/bin/freeview | grep not If you see output that says a library was not found, then something is not right with your system - which could explain the segfault. In that case I would try to find a way to download and install the freesurfer 7.2.0 Debian package installer as that should install any missing libraries.https://secure-web.cisco.com/17qbBdi-wXIfcvgJHoFSyqwZNNfccEzYQiqaLM3KKP1GfRbI3U94aISVOv9a0YGhQd-FCtmmbw7EmGlkXloHQKHGR5kQ0Ohxp0JGux2qcz8j5Rt8B1ctRfTvIV0UnaEl1nURjUsgCYtjC_sdG7KQX4ngvB3LSoCGEbOfNmi6oSxEaLWw_txh_79zUoOTNlVLgJDc-Aiw0gVqTJZNFknHkH8hauq6pkHSeBkQOXmK_JglhjC6WkKJ7lxYocce_WbdghbeaKkfQAYCYs_29qmOAYZN6dGIMzsWXk3nEcX4_2o-8BIcJbPHPV8yjzL-ug7MmedUYalixU7ncC7ps_gf7gA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer-linux-ubuntu18_amd64-7.2.0.tar.gz If no libraries are reported as missing for freeview, then if you have not already tried the variations on setting DISPLAY listed at the end of this page, then I would do so, https://secure-web.cisco.com/1ZTeXQ90uTtWNjlyitGyKt3hbJVwUsSL_sYysu7DQgUWeVYEJ3df0g2306v_BSgfcZcf-O-h84P8FI1bM8w6NvXdRDfn8OmNn3Bd2V_G3xAgU6xj4cUCTfEb713wXDGFlgtPBlmY8DpBUgV5sW4LgTOtwmG4nrBFDvr7sTDlSADHJxgc65FfWf__QvgO9AXBeGjue8kk34zd9MWvvU4rcxgnyVLxMPmKN4iPYD0FXifn62v010k6baCbhiM-My8JXv-HZT-AtXOYDaZqqe6lpOJxP5BDg8rXv8rApcm1Xiy-kKg73gkr8CeS_jMpXPsNPuk9XGaMpHUUQWsSXV1Cbnw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFS7_wsl_ubuntu You may have to use your IP address and append :0 or :1 to it. If that does not work, then send back your default setting for DISPLAY and I will check with other people who use the WSL setup. - R.
On Nov 17, 2021, at 21:02, 许霄 <xux...@xii.ac.cn> wrote: External Email - Use Caution I downloaded a license file, and copied the content in it to a new file created in $HOME path, named the new file 'license.txt'. After that, reset the environment variables:$ echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc$ echo "export DISPLAY=:0" >> $HOME/.bashrc$ echo "export FREESURFER_HOME=/usr/local/freesurfer/7-dev" >> $HOME/.bashrc$ echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc$ echo "source /usr/local/freesurfer/7-dev/SetUpFreeSurfer.sh" >> $HOME/.bashrcMeanwhile, to test if Xming was running, I executed xeyes, and it worked. But the same error "Segmentation fault (core dumped)" still appeared. I found that there was no .xdg file under $HOME path, mentioned in the command"export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc". Please see the details in the attachment. What should I do to fix it?Best Xiao-----原始邮件-----发件人:fsbuild <fsbu...@contbay.com>发送时间:2021-11-18 03:05:29 (星期四)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xux...@xii.ac.cn主题: Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped) External Email - Use Caution Hello, Xuxiao,You need to go to this URL, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-AZrSjO8Cl_Hc1uoojvBIGTFics6sBFWG99iZ-P1u3LukFGKniPlUm-E-VGjcRE_b-5E-iOvjqEZNnuGOgCw2Pkg1-eC-UxfUhNvM4PC4oeD-yGP31_5V7cBwdiywW09KhcDihFjOvJSLlMoqKyKIkSMftWf7jNXb3CzOUgWTiSKzJ6V7cP5ooLjf7jC6_Z2fma3-7ssLtdEbEYZL3t9_hHSX43mODgn8iO_TikKgwbVAJLuq6_dxHjhTZd2oIhm1adZDW1MzIDHvFsP_f9Gx49oAoTHPuuFB7gACzq83ISkU93lG2zQlUZjeTqIoCu3Y65c2oY5Pd95FlbeLROCOg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html, fill out the form and agree to the terms of the freesurfer license. Then you will be able to download a license file.- R.On Nov 17, 2021, at 06:10, 许霄 <xux...@xii.ac.cn> wrote: External Email - Use Caution Hello FreeSurfer Developers, According to your reply, I found that xeyes worked, but there was no license file. I thought the license file would be created automatically after installation of freesurfer, or by the command "echo "export FS_LICENSE=$HOME/license.txt" >> $HOME/.bashrc". Do I need to create a license file manually?-----原始邮件-----发件人:fsbuild <fsbu...@contbay.com>发送时间:2021-11-17 10:16:00 (星期三)收件人: freesurfer@nmr.mgh.harvard.edu抄送: xux...@xii.ac.cn主题: Re: [Freesurfer] freeview error after installation: Segmentation fault(core dumped) / free( ): invalid pointer, Aborted(core dumped) External Email - Use Caution Hello Xuxiao, In a terminal window in Ubuntu running under WSL, please try just running a simple X windows program like xeyes to test that your X-server is running on Windows, $ xeyes(see attachment for what it should look like)Keep an eye out for a flashing X server icon at the bottom of your Windows desktop. You may have to click on that flashing icon for the xeyes X window to open. But if you can’t display something simple like xeyes with the X server on Windows 10, then freeview is not going to work.If you installed the Xming X-server on Windows, then you should see an X icon on your desktop that you can click on to start the X-server. And you can check you see the X icon in the “hidden” area at the bottom of the screen which shows the X server is running on Windows. See the bottom of this page for how to see Xming is running and then scroll up to see the X windows desktop icon, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1TBZgGoCMRxatsJxkiVLCRpMVWvUvFkTaOzcvQfJ7zsWEbJbr6kfpyQw9rXePJDhX2Uqm1y0HM9GPCl8mJeBYFlC4drX30LHMKRV3lynvPnpHFk3ys6dOgFB1qlOF1OU0U-8rAESjQvPCztebrSgmqxcZzVRKDzPzcEWgKrMnUkVI79J8qlZjIxGnuk1i-Pj6wCdJZpvTM0wujOGuZqY314ieYSLo0j3Jk3GtZ-Vy2KLuqUK11QQwqIzE2dJ-QEbIoUKo0IJxXZcsBpYGWtjfQs9thrVHa9Zf37AqasPN48pzWeD-CJ5xBMUCHVq-Ynt7VH6noKWC3KONLoSj2bUjCQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFSL_wsl_xmingIf xeyes works, then check your freesurfer license file can be found. One way to do that is to set the environment variable FS_LICENSE to the absolute path to your license file. So you could for example call your license file “license.txt” and copy it into your home directory (denoted by the environment variable $HOME). You can also set FS_LICENSE in your shell init file.$ cd $HOME$ pwd<output deleted>$ ls license.txtlicense.txt$ export FS_LICENSE=$HOME/license.txt… check it can be read …$ cat $FS_LICENSE<output deleted>Now set FREESURFER_HOME, source the setup environment script as you did in the screenshot you sent below, and try running freeview with no arguments to see if a blank window opens.$ freeviewAnother thing to consider is to try and install the latest version of freesurfer (7.2.0) using the Ubuntu .deb package installer from https://secure-web.cisco.com/1bD8OkPccvOAmV7HP2pmcm7yP9Bsy6_MyEW01eJ2F-rwfjk4eaxq-YKetmfUNiJykhYrMKL61cKvpULEL8Jh8nExudxRoBPl379QTepkyrxKtwrk7Dy9eGOiPGa7IsG-RRbeqAPm-DUQ7-M7_PdD7hr5HAKQtMRgE6MIbhMNEjiZIKFpbQTay190OKqTgINkf3s0tUlShLRcbILiJ0qwzbBgGo7xF1W719V-X8FW7BY8btGVCpPQBGeA7ufue0A7KgbSzmUGENLpLWZ2ZgRU7GbiaRERepaAUHt4yi1geWOdTWntWTg9Nlm2TJZA1t1WXDo3WIzy68T7opQIFDlyWVg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.2.0%2Ffreesurfer_7.2.0_amd64.deb and install it with,$ sudo apt-get install ./freesurfer_7.2.0_amd64.debThen you should see 7.2.0 installed as something like /usr/local/freesurfer/7.2.0 which you would use for FREESURFER_HOME- R.On Nov 16, 2021, at 07:26, 许霄 <xux...@xii.ac.cn> wrote: External Email - Use Caution Hello FreeSurfer Developers,I can't access the website of archives, so I have to ask questions in this way. I installed freesurfer7-dev in Ubuntu18 in wsl according to the tutorials FS7_wsl - Free Surfer Wiki (harvard.edu) and FS7_wsl_ubuntu - Free Surfer Wiki (harvard.edu). After adding the license, when I tried to run the 'freeview' command to test if everything works well, an error popped out: Segmentation fault(core dumped). more information about my freesurfer environment is shown as attached. Could anyone help me figure it out? Thanks in advance.<freeview-Segmentation fault.png>_______________________________________________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<bug.png>_______________________________________________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
