<div dir="ltr">Hello all,<div><br></div><div>Thanks for the comments! Sorry for not being more precise. I installed FSL from the neurodebian repo, and all the normal stuff works fine. The good folks at FMRIB have sent me some experimental analysis tools that require setup and compiling. I could not get them to compile using the files and instructions they sent. The readme essentially says to untar the folder (which contains a makefile, dependencies, etc), run </div>
<div><br></div><div>$ . setup.sh </div><div><br></div><div>, then run </div><div><br></div><div>$ make </div><div><br></div><div>It seems that my installation is lacking "a compatible devel package", which has the default make, config, and include files that the setup scripts were expecting.</div>
<div><br></div><div>I've been told that I have two options:</div><div><br></div><div>1. Uninstall neurodebian FSL and try to build the source FSL myself</div><div>2. Download the source version of FSL, then customize those config files to match the neurodebian libraries and executables</div>
<div><br></div><div>My questions would more precisely have been stated as:</div><div><br></div><div>1. Does neurodebian already have the FSL devel package? If so, how can I install it?</div><div>2. If not, is there documentation on editing source FSL config files to work with neurodebian?</div>
<div><br></div><div>I've attached the makefile, in case that will be of any help. </div><div><br></div><div>Running:</div><div>$ sudo apt-get build-dep fsl</div><div>throws this dependency error:</div><div><The following packages have unmet dependencies:</div>
<div> libgd2-noxpm-dev : Depends: libgd2-noxpm (= 2.0.36~rc1~dfsg-6ubuntu2) but it is not going to be installed</div><div>E: Build-dependencies for fsl could not be satisfied.></div><div><br></div><div>Thanks again for your help,</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><font color="#666666" face="arial, helvetica, sans-serif"><a href="http://deniederhut.strikingly.com" target="_blank">deniederhut.strikingly.com</a></font></div>
</div></div>
<br><br><div class="gmail_quote">On Thu, Jun 19, 2014 at 5:51 AM, Yaroslav Halchenko <span dir="ltr"><<a href="mailto:debian@onerussian.com" target="_blank">debian@onerussian.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div class="HOEnZb"><div class="h5"><br>
On Thu, 19 Jun 2014, Yury V. Zaytsev wrote:<br>
<br>
> On Wed, 2014-06-18 at 10:17 -0700, Dillon Niederhut wrote:<br>
<br>
> > Is there a devel package for Debian around somewhere that I missed? If<br>
> > not, would anyone be willing to provide some advice to a Linux novice<br>
> > about the sorts of configuration changes I'll need to make around<br>
> > executables and libraries in the source FSL make and setup files?<br>
<br>
> I didn't quite understand your problem, but it seems to me that you are<br>
> trying to build FSL from source, having previously installed it from<br>
> NeuroDebian in form of binary packages. This didn't work, because<br>
> apparently you don't have all the dependencies installed.<br>
<br>
> Is this summary correct?<br>
<br>
> If yes, then you could use apt-get to automatically install packages<br>
> that are needed to build FSL (this is how NeuroDebian FSL is built):<br>
<br>
> apt-get build-dep fsl<br>
<br>
</div></div>and<br>
<br>
apt-get source fsl<br>
<br>
to obtain all the sources you could then build using e.g.<br>
dpkg-buildpackage<br>
<br>
Note #1, that for those two commands you need to uncomment deb-src lines in<br>
your neurodebian /etc/apt/ file and run apt-get update first.<br>
<br>
Note #2, fslview is packaged separately<br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
Yaroslav O. Halchenko, Ph.D.<br>
<a href="http://neuro.debian.net" target="_blank">http://neuro.debian.net</a> <a href="http://www.pymvpa.org" target="_blank">http://www.pymvpa.org</a> <a href="http://www.fail2ban.org" target="_blank">http://www.fail2ban.org</a><br>
Research Scientist, Psychological and Brain Sciences Dept.<br>
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755<br>
Phone: <a href="tel:%2B1%20%28603%29%20646-9834" value="+16036469834">+1 (603) 646-9834</a> Fax: <a href="tel:%2B1%20%28603%29%20646-1419" value="+16036461419">+1 (603) 646-1419</a><br>
WWW: <a href="http://www.linkedin.com/in/yarik" target="_blank">http://www.linkedin.com/in/yarik</a><br>
<br>
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</font></span></blockquote></div><br></div>