[Neurodebian-users] Command line issues with FSL

[Dillon Niederhut]

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>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
> >:
>
>> 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
>> 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
>
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