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, https://secure-web.cisco.com/1OO6_69UmGU84poSsYr7cookfWG3oW-9wCm0t5GqC3v9O7o... If 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. $ freeview Another 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/1WCN8dpJeL5ctI2hET4QOYyxIu9gxAiTFJ_bFQH-ZV0hRCj... and install it with, $ sudo apt-get install ./freesurfer_7.2.0_amd64.deb Then 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 <xuxiao@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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 fsbuild@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: xuxiao@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/1ysFQMH5-3PjGsAtjRCyqR6tLEu576gjQo1Oa6S4YqfU8M4...
If 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.txt license.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.
$ freeview
Another 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/1vUB0SIgaD7Aa_vdzXHRIqptu1j91bTzpsQFynE-rpn8jtl... and install it with,
$ sudo apt-get install ./freesurfer_7.2.0_amd64.deb
Then 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 xuxiao@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 list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1dWhyPS-KCpAkRXuNYV7jS4mkrkxfdk1QgZeSNSZXoCHCB2...
freesurfer@nmr.mgh.harvard.edu
-
fsbuild -
许霄