[Neurodebian-users] Command line issues with FSL

[Williams, Travis]

Hi there,

I don't think you wanted to do that with the PATH: directive. You want to add a 'source' to your login scripts.

So if there is a "/etc/fsl/5.0/fsl.sh" file (check that it is in fact there) then you want to add the following line to the END of your .bashrc file in your home directory:

source /etc/fsl/5.0/fsl.sh

Then save, log out and log back in, or just open and close the terminal or type: hash -r and see if you can then see the fsl programs.

You can also (if you have root access and intend for several users to use the fsl programs) add the 'source /etc/fsl/5.0/fsl.sh' line to the end of the /etc/bash.bashrc file.

Hope that helps.

~Travis Williams
IS Manager 1
Neurology Department,
Medical College of Wisconsin
________________________________
From: Neurodebian-users [neurodebian-users-bounces+trwilliams=mcw.edu at lists.alioth.debian.org] on behalf of Dillon Niederhut [dillon.niederhut at berkeley.edu]
Sent: Thursday, March 13, 2014 10:58 AM
To: Kiyotaka Nemoto
Cc: neurodebian-users at lists.alioth.debian.org
Subject: Re: [Neurodebian-users] Command line issues with FSL

Hi Kiyotaka,

Thanks for your reply. As I said above, I'm not very familiar with Unix systems. I tried adding ". /etc/fsl/5.0/fsl.sh" to the end of the file. I logged out and logged back in, and still could not access command line functions.

I looked up how to edit .profile and add paths in the Ubuntu help pages<http://askubuntu.com/questions/tagged/.profile>, and added the above path for FSL to the end of the .profile file using something like PATH="PATH:$. /etc/fsl/5.0/fsl.sh". I logged out of the system, but now I cannot log back in.

I'll try to edit out the new lines via the command prompt in recovery mode. In the mean time, any help with the correct syntax would be greatly appreciated.

Thanks,
Dillon

Dillon Niederhut
Doctoral Candidate
University of California, Berkeley
Department of Anthropology
232 Kroeber Hall
Berkeley, CA 94720


On Thu, Mar 13, 2014 at 12:58 AM, Kiyotaka Nemoto <kiyotaka at nemotos.net<mailto:kiyotaka at nemotos.net>> wrote:
Dear Dillon,

The solution is simple and written in the FSL website.

http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux


Quick start for Debian/Ubuntu users

As of fsl 5.0 all you need do is add ". /etc/fsl/5.0/fsl.sh" to the end of your .profile file. When you next login you should find the fsl programs are available.


Hope this helps,

Kiyotaka





2014-03-13 15:03 GMT+09:00 Dillon Niederhut <dillon.niederhut at berkeley.edu<mailto:dillon.niederhut at berkeley.edu>>:
Hello everyone,

I have FSL 5.0.6 installed on Ubuntu 12.0.4LTS through the neurodebian repository. The GUI works just fine, but when I try to run commands through the terminal, I consistently get errors saying the command cannot be found. This is true for starting the FSL GUI through the command line, and every command for structural imaging. diffusion imaging, and brain extraction. The only exception is FSLView, which seems to work just fine from the command line.

I tried uninstalling and reinstalling the FSL core, which hasn't helped. I've dug around a bit through the google search results for this issue, but trying different command names hasn't helped either. I found a few archived email exchanges talking about configuring bash files, but I don't know enough about unix to know what this is. Can anyone help?

Thanks,
Dillon

Dillon Niederhut
Doctoral Candidate
University of California, Berkeley
Department of Anthropology
232 Kroeber Hall
Berkeley, CA 94720


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--
Kiyotaka Nemoto, M.D., Ph.D.
Assistant Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyotaka at nemotos.net<mailto:kiyotaka at nemotos.net>