Re: [Freesurfer] Freesurfer installation issue

External Email - Use Caution  Try using apt to do the install, and you could also preface the package name with its absolute path, /path/to/package $ sudo apt install /path/to/package/freesurfer_7.2.0_amd64.deb - R. On Jul 15, 2023, at 05:02, Ramesh Babu

[Freesurfer] Freesurfer installation issue

External Email - Use Caution Dear Expert, I am trying to install Freesurfer-7.2 .deb package. I had this package earlier, and after formatting my system now, I am trying to install Freesurfer again. But I am facing the following issues. 'freesurfer_7.2.0_amd64.deb' is not a Debia

[Freesurfer] Freesurfer installation help

External Email - Use Caution You seriously need to improve the installation help for non-linux experts. I spent six hours trying to upgrade from 7.3.2 to 7.4.1. The first 40 minutes was going through your help pages and reading very carefully starting here: https://secure-web.cis

[Freesurfer] Freesurfer installation

External Email - Use Caution Dear Freesurfer developers, For the installation of Freesurfer, I'd need a pass code to extract the zip file. Best regards Stefan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m

Re: [Freesurfer] FreeSurfer installation in a Code Ocean Capsule

External Email - Use Caution Hello Chiara, It reads like Code Ocean wants to be a solution for someone to host all their research files for published articles, scripts, applications and binaries to run - in 1 place.  But it’s not clear to me applications/scripts/binaries can be

[Freesurfer] FreeSurfer installation in a Code Ocean Capsule

External Email - Use Caution Dear Freesurfer, I am trying to use some FreeSurfer tools inside a Code Ocean capsule (https://secure-web.cisco.com/1F1n6n0E7KQZBogoJ-y7cciJe_z3d-WxxhEPHp2zwkasImEBZvKePlK6P71av7i50AM4Z0TPRLdriPQ7fWxL-OnFfVOJBHQItgkdxdjByqeRfMyJTCMrcEaYvsJALn5

[Freesurfer] freesurfer installation pass code request

External Email - Use Caution Hi, I have downloaded the Freesurfer Virtualbox VM images. Would you please send me the pass code? Sincerely, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

Re: [Freesurfer] Freesurfer installation error?

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer installation error? External Email - Use Caution Hello, Please see the following installation I attempted. banikr2@banikr:~$ which yum I already had a previous faulty freesurfer installed. banikr2@banikr:~$ ls -l -h drwxrwsr-x 17

Re: [Freesurfer] Freesurfer installation error?

24 13:17 freesurfer-linux-centos6_x86_64-7.1.1.tar.gz The same error persists. Rana Banik From: fsbuild Sent: Saturday, September 25, 2021 8:23 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Banik, Rana Subject: Re: [Freesurfer] Freesurfer installation error? It lo

Re: [Freesurfer] Freesurfer installation error?

External Email - Use Caution It looks like you want to install and run the 7.1.1 release on CentOS6. The fsfast and mni subdirectories are in the distribution, so I am not sure why you are getting that output.  I suggest trying to do a clean install from scratch.  There are a cou

[Freesurfer] Freesurfer installation error?

External Email - Use Caution Installed freesurfer with the following errors. banikr2@banikr:~/freesurfer$ source $FREESURFER_HOME/SetUpFreeSurfer.sh freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 Setting up environment for FreeSurfer/FS-FAST (and FSL) WAR

Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine

External Email - Use Caution I should have said at the end for installation under $HOME to set, $ export FREESURFER_HOME=$HOME/freesurfer - R. fsbuildMarch 3, 2020 at 15:39 External Email - Use Caution Hello Ben, For packag

Re: [Freesurfer] Freesurfer installation on Ubuntu virtual machine

External Email - Use Caution Hello Ben, For packages to install, see the following wiki page, https://surfer.nmr.mgh.harvard.edu/fswiki/BuildRequirements Usually to expand the freesurfer *.tar.gz archive under /usr/local, you would need sudo/root privileges, e.g. $ cd /usr/local

[Freesurfer] Freesurfer installation on Ubuntu virtual machine

External Email - Use Caution Dear Freesurfer experts, Even though this problem has been raised in the archives, I was not able to find a specific solution to my problem. I installed Freesurfer on a virtual machine which runs Ubuntu 18.04.4 (Host system: Windows 10). But it seems

Re: [Freesurfer] FreeSurfer Installation

try this page: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall#FreeSurferDownloadandInstall cheers Bruce On Mon, 22 Jan 2018, Caio Quini wrote: > Hello > > I am trying to download FreeSurfer from freesurfer.net and I can't open the > download page. > It keeps returning an error mes

[Freesurfer] FreeSurfer Installation

Hello I am trying to download FreeSurfer from freesurfer.net and I can't open the download page. It keeps returning an error message. Is that a common error? Is there any other way to download the software? Thank you very much. Regards Caio Quini ___

[Freesurfer] freesurfer installation through Virtual-box

Sir, I would like to install the Virtualbox version of freesurfer in XUBuntu platform, version V5.3.0. However whenever I am clicking the link for this, the download page which is opening is crashing. I have tried in other systems. The Internet connection is also very good here. The page tha

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 not

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 the

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

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 a

[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 freesurfer-Linux-centos4_x86_64-stable

Re: [Freesurfer] FreeSurfer installation

Hi Neda, Your terminal is probably setup to use the bash environment by default. If you type tcsh, then you'll be using C shell and that command should then work. I see that this is not on the install page, but on the setup/config page there is a note about it. There are also alternate comma

Re: [Freesurfer] FreeSurfer installation

Hi dear Louis, yes I read this link https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall but when I write this command setenv FREESURFER_HOME /usr/local/freesurfer I see this message: bash: setenv: command not found best, Neda On Wed, Jan 22, 2014 at 9:06 PM, Louis Nicholas Vinke < vi...@nmr

Re: [Freesurfer] FreeSurfer installation

Hi Neda, Have you read over the linux install directions in the link below? You will need to register and get a license file. After that you should look over the setup and config instructions. https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall https://surfer.nmr.mgh.harvard.edu/fswiki/Setu

[Freesurfer] FreeSurfer installation

Hi dear all, I want to use freesurfer for tractography by FSL. I downloaded freesurfer-linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz and I want to install it but I don't know how. Please help me. Thanks in advance, Neda ___ Freesurfer mailing list Frees

Re: [Freesurfer] Freesurfer installation error

solved, thank you, Octavian On Sat, Dec 21, 2013 at 11:55 AM, Octavian Lie wrote: > Dear All, > > I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version > (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf > libraries missing in my distro, here is fs home direct

[Freesurfer] Freesurfer installation testing tksurfer error

Dear All, I have recently upgraded freesurfer (dev version 12/19/2013 centos6, 86X64) on my ubuntu 12.04 box, I previously used v 5.1(centos 4). I fixed all other issues that I posted about (libnetcdf missing,.tcshrc editing), now all seems to go well, including testing, except when I load tksur

[Freesurfer] Freesurfer installation error

Dear All, I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf libraries missing in my distro, here is fs home directory: FREESURFER_HOME /usr/local/fs5.3/freesurfer FSFAST_HOME /usr/local/fs5.3/freesur

Re: [Freesurfer] Freesurfer installation

Pablo, That page "describes how to setup a personal laptop for usage in the Freesurfer course." It does not apply to a standard freesurfer installation. Try opening a new terminal and typing "bash" before the "export" and "source" commands you give below. -Zeke On 07/17/2013 10:27 AM, pablo

[Freesurfer] Freesurfer installation

Dear Freesurfer experts, I have a question regarding the installation/running of FreeSurfer. I have been trying to install freesurfer in a macbook pro (snow leopard) but no success. I followed the webpage from freesurfer (link below). https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Perso

[Freesurfer] freesurfer installation (fail)

Hello there, I''ve tried a couple installations of FreeSurfer as listed on the website. Though there seems to be a problem. Both linux tarballs seem to be designed for centos4, though that version is not supported anymore, so downloading is a pain, and accessing packages is out of the question.

[Freesurfer] freesurfer installation (fail)

Hello there, I''ve tried a couple installations of FreeSurfer as listed on the website. Though there seems to be a problem. Both linux tarballs seem to be designed for centos4, though that version is not supported anymore, so downloading is a pain, and accessing packages is out of the question.

Re: [Freesurfer] Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context

this info might help: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11934.html On Tue, 2010-12-07 at 13:58 -0500, dah...@nmr.mgh.harvard.edu wrote: > Hi, > > Would really appreciate help with this insallation problem! > > I'm installing freesurfer on a new system, and at an init

[Freesurfer] Freesurfer installation on RHEL 5.4: failed to create OpenGL rendering context

Hi, Would really appreciate help with this insallation problem! I'm installing freesurfer on a new system, and at an initial test running "tkmedit bert.mgz" produces GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context. I thought maybe updating the NVidia card would help,

Re: [Freesurfer] [freesurfer] installation

Is that file in that directory? What size is it? Do you have write permissions to that folder? doug Ignacio Letelier wrote: > Hi all > > I'm a new freesurfer user and I have some troubles installing the > program. > > after moving to > cd /usr/local > > I typed *freesurfer-virtual:~>* tar xzvf

[Freesurfer] [freesurfer] installation

Hi all I'm a new freesurfer user and I have some troubles installing the program. after moving to cd /usr/local I typed *freesurfer-virtual:~>* tar xzvf freesurfer-Linux---full.tar.gz replacing - with freesurfer-Linux-centos4-stable-pub-v4.3.1 I get the following error message Cannot >>

[Freesurfer] [freesurfer] installation failure

Dear freesurfer experts, I'm running into installation failure and can't quite figure this out (I'm a novice Linux user too). It complains there is no such file or directory when I simply followed the instruction by typing the command below in the /usr/local directory. tar xzvf freesurfer-L

[Freesurfer] Freesurfer installation on Ubuntu

Hello FS experts, I am trying to install FS on Ubuntu 9.04. I am testing the installation as suggested in your website, and found the following message when attempting to start the qdec application: **

Re: [Freesurfer] Freesurfer installation on Ubuntu desktop or server?

Yes, everything Rudolph said. Also, the FreeSurfer we package for Ubuntu is actually a CentOS build because Ubuntu is a flavor of linux like CentOS and since FreeSurfer package is self-contained everything should work once you un-tar-gz. The only things we don't bundle are X server and OpenGL

Re: [Freesurfer] Freesurfer installation on Ubuntu desktop or server?

Burcu Ays,en Ürgen wrote: > Hi all, > > If one installs Freesurfer on Ubuntu, should he/she prefer the desktop > version of Ubuntu or server edition? Does it matter? > From FreeSurfer's perspective, it doesn't matter all that much if at all -- depends more on what other tasks you want the machin

[Freesurfer] Freesurfer installation on Ubuntu desktop or server?

Hi all, If one installs Freesurfer on Ubuntu, should he/she prefer the desktop version of Ubuntu or server edition? Does it matter? Thank you, Burcu Aysen Urgen. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.ed

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

autoredraw on does not help. i don't know whether i'm using vmware or virtualbox. can anyone comment on how to check that and whether this should solve the problem? thanks!!! > Can you post the output of dmesg command? > Are you using vmware? TkSurfer works fine in Virtualbox (2.1.4) but I'm >

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

Can you post the output of dmesg command? Are you using vmware? TkSurfer works fine in Virtualbox (2.1.4) but I'm not sure it'll do in current vmware. If you are using it I suggest you to migrate your virtual machine to VirtualBox: http://www.virtualbox.org/ Have you tried setting the autoredraw o

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

that did not work. (thanks for trying, and yes, i'm using tcsh) > If you are using tcsh > > setenv doublebufferflag 1 > > in bash > > export doublebufferflag=1 > > --- > Pedro Paulo de M. Oliveira Junior > Diretor de Operações > Netfilter & S

Re: [Freesurfer] Freesurfer installation: tksurfer not drawing

If you are using tcsh setenv doublebufferflag 1 in bash export doublebufferflag=1 --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br On 1 de abril de 2009

[Freesurfer] Freesurfer installation: tksurfer not drawing

Hi, I've installed freesurfer on my Stanford linux machine, and while checking it can see subject bert in tkmedit. However, tksurfer isn't drawing in its window, and there's an error message surfer: ### redraw failed: no gl window open The installation is over Fedora Core 6 (build x86_64) How d

Re: [Freesurfer] Freesurfer Installation on Ubuntu 6.06

Hema, What is your DISPLAY environment variable set to? That is, what is the output of: echo $DISPLAY it should be something like: :0.0 Nick On Sun, 2008-12-14 at 17:16 -0500, Hemalatha Sampath wrote: > Hi, > > I am trying to install freesurfer on Ubuntu 6.06 32 bit processor machine. I

[Freesurfer] Freesurfer Installation on Ubuntu 6.06

Hi, I am trying to install freesurfer on Ubuntu 6.06 32 bit processor machine. I have downloaded the centos4-stable-pib-v4.1.0 and followed the installation instructions. I am installing it through remote login via ssh. During testing the installation by executing the tkmedit bert sample-001.mg

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 OS

[Freesurfer] Freesurfer Installation Problem

I recently installed FreeSurfer 3.0.4 for CentOS 4 x86_64 on a server running Fedora Core 3 (w/ x86_64), but ran into the following error upon testing the installation with the command "tkmedit bert orig.mgz": $ tkmedit bert orig.mgz Talairach transform /autofs/space/freesurfer/subjects/bert/

Re: [Freesurfer] freesurfer installation problems

Hi Chacko, FREESURFER_HOME is an environment variable you need to set to point to the place that you intalled FreeSurfer. Bruce On Tue, 16 May 2006, Chacko Cherian wrote: Hello all, I am having some trouble in using the freesurfer version I had downloaded.The FREESURFER_HOME file is missi

[Freesurfer] freesurfer installation problems

Hello all, I am having some trouble in using the freesurfer version I had downloaded.The FREESURFER_HOME file is missing and so I cannot source or setenv anytime I want to use it.Do I need to tar and unzip again or is there any other way? Thanks in advance Chacko. ___