<div dir="ltr">Hi Kiyotaka,<div><br></div><div>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.</div>
<div><br></div><div>I looked up how to edit .profile and add paths in the <a href="http://askubuntu.com/questions/tagged/.profile">Ubuntu help pages</a>, 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.</div>
<div><br></div><div>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.</div><div><br></div><div>Thanks,</div><div>
Dillon</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><font color="#666666" face="arial, helvetica, sans-serif">Dillon Niederhut</font><div><font color="#666666" face="arial, helvetica, sans-serif">Doctoral Candidate</font></div>
<div><font color="#666666" face="arial, helvetica, sans-serif">University of California, Berkeley</font></div><div><font color="#666666" face="arial, helvetica, sans-serif">Department of Anthropology</font></div><div><font color="#666666" face="arial, helvetica, sans-serif">232 Kroeber Hall</font></div>
<div><font color="#666666" face="arial, helvetica, sans-serif">Berkeley, CA 94720</font></div></div></div>
<br><br><div class="gmail_quote">On Thu, Mar 13, 2014 at 12:58 AM, Kiyotaka Nemoto <span dir="ltr"><<a href="mailto:kiyotaka@nemotos.net" target="_blank">kiyotaka@nemotos.net</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr"><div><div>Dear Dillon,<br><br></div>The solution is simple and written in the FSL website.<br><br><a href="http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux" target="_blank">http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux</a><br>
<br><p><strong>Quick start for Debian/Ubuntu users</strong> <span></span><span></span></p><p>As of fsl 5.0 all you need do is add "<tt>. /etc/fsl/5.0/fsl.sh</tt>" to the end of your .profile file. When you next login you should find the fsl programs are available. </p>
<br></div><div><br>Hope this helps,<br><br>Kiyotaka<br><br><br></div><div><div><div><div><br></div></div></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">2014-03-13 15:03 GMT+09:00 Dillon Niederhut <span dir="ltr"><<a href="mailto:dillon.niederhut@berkeley.edu" target="_blank">dillon.niederhut@berkeley.edu</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div class="h5"><div dir="ltr">Hello everyone,<div><br></div><div>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. </div>
<div><br></div><div>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?</div>
<div><br></div><div>Thanks,</div><div>Dillon</div><span><font color="#888888"><div><br clear="all"><div><div dir="ltr"><font color="#666666" face="arial, helvetica, sans-serif">Dillon Niederhut</font><div><font color="#666666" face="arial, helvetica, sans-serif">Doctoral Candidate</font></div>
<div><font color="#666666" face="arial, helvetica, sans-serif">University of California, Berkeley</font></div><div><font color="#666666" face="arial, helvetica, sans-serif">Department of Anthropology</font></div><div><font color="#666666" face="arial, helvetica, sans-serif">232 Kroeber Hall</font></div>
<div><font color="#666666" face="arial, helvetica, sans-serif">Berkeley, CA 94720</font></div></div></div>
<div dir="ltr"><br></div></div></font></span></div>
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</font></span></blockquote></div><span class="HOEnZb"><font color="#888888"><br><br clear="all">
<br>-- <br>Kiyotaka Nemoto, M.D., Ph.D.<br>Assistant Professor<br>Department of Psychiatry<br>Division of Clinical Medicine, Faculty of Medicine<br>University of Tsukuba<br>1-1-1Tennodai Tsukuba, Ibaraki 305-8575, Japan<br>
E-mail: <a href="mailto:kiyotaka@nemotos.net" target="_blank">kiyotaka@nemotos.net</a>
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