[Neurodebian-users] Developer files for Debian FSL

[Dillon Niederhut]

Hello all,

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

$ . setup.sh

, then run

$ make

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.

I've been told that I have two options:

1. Uninstall neurodebian FSL and try to build the source FSL myself
2. Download the source version of FSL, then customize those config files to
match the neurodebian libraries and executables

My questions would more precisely have been stated as:

1. Does neurodebian already have the FSL devel package? If so, how can I
install it?
2. If not, is there documentation on editing source FSL config files to
work with neurodebian?

I've attached the makefile, in case that will be of any help.

Running:
$ sudo apt-get build-dep fsl
throws this dependency error:
<The following packages have unmet dependencies:
 libgd2-noxpm-dev : Depends: libgd2-noxpm (= 2.0.36~rc1~dfsg-6ubuntu2) but
it is not going to be installed
E: Build-dependencies for fsl could not be satisfied.>

Thanks again for your help,
Dillon

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


On Thu, Jun 19, 2014 at 5:51 AM, Yaroslav Halchenko <debian at onerussian.com>
wrote:

>
> On Thu, 19 Jun 2014, Yury V. Zaytsev wrote:
>
> > On Wed, 2014-06-18 at 10:17 -0700, Dillon Niederhut wrote:
>
> > > Is there a devel package for Debian around somewhere that I missed? If
> > > not, would anyone be willing to provide some advice to a Linux novice
> > > about the sorts of configuration changes I'll need to make around
> > > executables and libraries in the source FSL make and setup files?
>
> > I didn't quite understand your problem, but it seems to me that you are
> > trying to build FSL from source, having previously installed it from
> > NeuroDebian in form of binary packages. This didn't work, because
> > apparently you don't have all the dependencies installed.
>
> > Is this summary correct?
>
> > If yes, then you could use apt-get to automatically install packages
> > that are needed to build FSL (this is how NeuroDebian FSL is built):
>
> >     apt-get build-dep fsl
>
> and
>
> apt-get source fsl
>
> to obtain all the sources you could then build using e.g.
> dpkg-buildpackage
>
> Note #1, that for those two commands you need to uncomment deb-src lines in
> your neurodebian /etc/apt/ file and run apt-get update first.
>
> Note #2, fslview is packaged separately
>
> --
> Yaroslav O. Halchenko, Ph.D.
> http://neuro.debian.net http://www.pymvpa.org http://www.fail2ban.org
> Research Scientist,            Psychological and Brain Sciences Dept.
> Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
> Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
> WWW:   http://www.linkedin.com/in/yarik
>
> _______________________________________________
> Neurodebian-users mailing list
> Neurodebian-users at lists.alioth.debian.org
> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
>
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