[Neurodebian-users] Command line issues with FSL

[Jeremy Gray]

Having locked myself out of an account before by messing with login
scripts, my advice is: after you change your login scripts (.profile, etc)
DONT logout to test them. Instead, while still logged in, try to establish
a second connection into the same account (e.g., via ssh). If that works,
great you are all set. If you can't login, not a problem because you are
still connected through the first connection and can revert things.

--Jeremy


On Thu, Mar 13, 2014 at 12:25 PM, Williams, Travis <trwilliams at mcw.edu>wrote:

> 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
>
>
> _______________________________________________
> Neurodebian-users mailing list
> Neurodebian-users at lists.alioth.debian.org<mailto:
> Neurodebian-users at lists.alioth.debian.org>
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
>
>
>
> --
> 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>
>
>
> _______________________________________________
> Neurodebian-users mailing list
> Neurodebian-users at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.alioth.debian.org/pipermail/neurodebian-users/attachments/20140313/9856d35d/attachment-0001.html>