Re: [Freesurfer] Installation problem

| sort thanks, Andrew From: Neda Mohammadi <n55moham...@gmail.com> Date: Sunday, March 11, 2018 at 6:30 AM To: "Hoopes, Andrew" <ahoo...@mgh.harvard.edu> Cc: FS Help <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Installation problem Hi Andrew, Than

Re: [Freesurfer] Installation problem

Hi Andrew, Thanks for your reply. It repeat the freesurfer startup message . freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast

Re: [Freesurfer] Installation problem

Hi Neda, What’s going on exactly? Is the source command hanging or is it repeatedly printing the freesurfer startup message? best Andrew On March 7, 2018 at 3:03:38 AM, Neda Mohammadi (n55moham...@gmail.com) wrote: Dear Expert, I tried to install Freesurfer

[Freesurfer] Installation problem

Dear Expert, I tried to install Freesurfer on Ubuntu 16.0.4. I've followed these steps: 1. Download and extract into the directory /usr/local 2.export FREESURFER_HOME=/usr/local/freesurfer Its fine, but when I run this step 3.source $FREESURFER_HOME/SetUpFreeSurfer.sh I receive this message n

Re: [Freesurfer] Freesurfer installation problem

Nick, Thanks very much. I will do as per your suggestion. I am new to Linux and Ubuntu. If I am not bothering you too much. I read an article where they compared the results from Freesurfer's different versions and about using different OS and concluded saying that use the same version and do

[Freesurfer] Freesurfer installation problem

Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing

Re: [Freesurfer] Freesurfer installation problem

Hi Venkat What hardware platform are you running on? And can you run: ls -l /usr/local/freesurfer/bin/mri_convert cheers Bruce On Tue, 10 Jun 2014, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am

Re: [Freesurfer] Freesurfer installation problem

Venkat, Your system appears to be 32bit distribution, as indicated by 'i686' in your output string, but the freesurfer you installed is 64b, indicated by 'x86_64' in our filename. So you will need the 32b dist: freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz Also, v5.0.0 is pretty old, I'd

Re: [Freesurfer] Freesurfer installation problem

Hi Bruce, Thanks very much What hardware platform are you running on? Memory: 3.8 GiB Processor Intel core i3-3220 cpu @3.30 GHz*4 Graphics Intel Ivybridge Desktop x86/MMX/SSE2 OS type 32-bit Disk 103.1 GB And can you run: ls -l /usr/local/freesurfer/bin/mri_convert I get the following when

Re: [Freesurfer] Installation problem on ubuntu 12.04.

Dear all, For the error freeview.bin: error while loading shared libraries: libjpeg.so.62: cannot open shared object file: No such file or directory sudo apt-get install libjpeg62 did the trick. Freeview is running fine For the error *libGL error: failed to load driver: swrast* *libGL

Re: [Freesurfer] Installation problem on ubuntu 12.04.

Markus, I have never seen those errors before. But a little googling suggested perhaps running the program as follows: ~$ LIBGL_DEBUG=verbose ./tkmedit bert orig.mgz Im a little at a lose at what else to try because we have freesurfer installed on pretty much stock Ubuntu platforms and it

Re: [Freesurfer] Installation problem on ubuntu 12.04.

Dear Zeke, Thanks for stepping in! $ LIBGL_DEBUG=verbose tkmedit bert orig.mgz libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/tls/swrast_dri.so libGL: OpenDriver: trying /usr/lib/x86_64-linux-gnu/dri/swrast_dri.so libGL error: failed to load driver: swrast Reading

[Freesurfer] Installation problem on ubuntu 12.04.

Dear experts! I installed freesurfer on a machine running Ubuntu 12.04. I have got some error messages when testing: ~$ freeview -v $SUBJECTS_DIR/bert/mri/norm.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f

Re: [Freesurfer] installation problem

Hello Xue, Via what method are you remotely accessing the Linux cluster? (VNC, cygwin, etc) I am not sure if it's your X client or the X server, but one of them, or maybe both, possibly lack support for OpenGL. If you aren't already using a VNC system that there I would try that option first.

Re: [Freesurfer] installation problem

thanks, Zeke I use SSH Secure Shell to make the connection, and before I have used xmanager(I was told xmanager can do OpenGL rendering on my local machine, the protocol I used in xmanager is also ssh), maybe the protocol is incorrect? does OpenGL have any hardware requirment? I'm wondering

Re: [Freesurfer] installation problem

I believe you are correct, that the poor card is the most likely culprit. The Matrox G200 range are not good at anything graphically intensive. If you have adequate permission you could try updating the drivers. (http://www.matrox.com/graphics/en/support/drivers/latest/) Also, try running

[Freesurfer] installation problem

dear freesurfer experts, I tried to install freesurfer in a remote linux cluster, when I completed the installation, and began to run the freesurfer gui use my own windows PC, the command line showed erro belowing information : [wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz GLUT: Fatal

Re: [Freesurfer] installation problem

file to the local folder.. Any idea of the problem of freesurfer in my computer? thanks Jie From: ni...@nmr.mgh.harvard.edu To: remembe...@hotmail.com Date: Wed, 23 Feb 2011 18:32:58 -0500 CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] installation problem

Re: [Freesurfer] installation problem

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] installation problem does mri_convert work? glxgears? tksurfer? qdec? freeview? your installation should work on ubuntu, as it has for other people, so i'm a bit at a loss. n. On Thu, 2011-02-24

Re: [Freesurfer] installation problem

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] installation problem does mri_convert work? glxgears? tksurfer? qdec? freeview? your installation should work on ubuntu, as it has for other people, so i'm a bit at a loss. n. On Thu, 2011-02-24 at 07:12 +0800, Liukarl wrote

Re: [Freesurfer] installation problem

what is the output of uname -a On Thu, 2011-02-24 at 00:53 +0800, Liukarl wrote: Hello, Freesurfer experts: I emailed some installation problems a couple days ago, but haven’t answered yet. I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system.

Re: [Freesurfer] installation problem in ubuntu

Dear Pedro, I would like to start with the tutorials but I don't have permission to copy the data to the subjects directory, how I can change this? Best regards, Carolina 2011/2/22 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br try the command: sudo apt-get install tcl --

Re: [Freesurfer] installation problem

#44-Ubuntu SMP Fri Jan 21 17:40:48 UTC 2011 i686 GNU/Linux thanks Jie Subject: Re: [Freesurfer] installation problem From: ni...@nmr.mgh.harvard.edu To: remembe...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Date: Wed, 23 Feb 2011 11:59:16 -0500 what is the output

Re: [Freesurfer] installation problem in ubuntu

try the command: sudo apt-get install tcl -- PPJ Please: cc the freesurfer list when answering 2011/2/22 Carolina Valencia cvalen...@linkdx.com.co Hi Pedro, Finally, I could install it with the license file and the environment is properly set without warnings. But trying to test it,

Re: [Freesurfer] installation problem in ubuntu

Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) WARNING:

Re: [Freesurfer] installation problem in ubuntu

Please send the result of the command: uname -a On Mon, Feb 21, 2011 at 10:31, Carolina Valencia cvalen...@linkdx.com.cowrote: Hi Bruce, I'm experimenting problems with the installation on Ubuntu too. There's is warning in the welcome message, it seems that something is missing:

Re: [Freesurfer] installation problem in ubuntu

It seems you are running the 64-bit version of FreeSurfer in a 32-bit OS 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Linux cvalencia-Precision-WorkStation-T3400 2.6.35-25-generic-pae #44-Ubuntu SMP Fri Jan 21 19:01:46 UTC 2011 i686 GNU/Linux Thanks, 2011/2/21 Pedro Paulo de

Re: [Freesurfer] installation problem in ubuntu

run this command sudo rm -rf $FREESURFER_HOME 2011/2/21 Carolina Valencia cvalen...@linkdx.com.co Thanks Pedro, How I uninstall that version to re-install the correct version? I look for some answers and try rm -rf $FREESURFER_HOME It says that I don't have permission,how I can

[Freesurfer] installation problem in ubuntu

Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and the only difference is that I installed it in my Documents, instead of local folder. Below

Re: [Freesurfer] installation problem in ubuntu

Hi Jie, what hardware are you using? Is it a 64 bit operating system? cheers Bruce On Sat, 19 Feb 2011, Liukarl wrote: Hello, Freesurfer experts: I am new to freesurfer and try to install the newest version of freesurfer in Ubuntu system. I closely followed the instructions, and

Re: [Freesurfer] Freesurfer Installation Problem

Jaakko, The message about the missing talairach.xfm file can be ignored (unless things stop completely and issue an error message). The code performs a relative path search to find the file if it doesnt find it in the hard- coded path (a historical remnant). About the Tcl problem, which Linux