[Neurodebian-devel] Adding a resting-state fMRI toolbox to the repository

[Yaroslav Halchenko]

On Tue, 29 Jul 2014, André Hoffmann wrote:
> > - fsl team introduced IMHO a minimal set of changes to it since
> >  the version in nifticlib and changes are not really that frequent

> I also just had a look at it and don’t think that my code would be affected by their changes, so migration to FSL should be quite painless.

> > - both fslio.c and fslio.h "has now been placed in the public
> >  domain.”

> What about this?

it is that you could just use them and there is really no licensing
issue

> >> Regarding the fslio library: the source code is actually still in the
> >> nifti source package, it is just not compiled, because the copyright is
> >> not cleared, see: 

> >> https://lists.debian.org/debian-legal/2006/09/msg00026.html

> > - they seems to be not using any other piece of FSL

> The includes for nifti1.h and znzlib.h (which also come with nifticlib) refer to paths within the FSL-codebase, but apart from that there seem to be no other dependencies.

> > - so theoretically (correct me if I am wrong), libfslio.so  could be
> >  also considered "GPL-compatible" and could be loaded at run time

> That still would require me to include fslio.h which I don’t believe is currently provided by any package or is it?

yeap.

> > So, I see two possibilities:

> > - Andre adjusts his code to just dlopen that library at run-time (given
> >  FSLDIR env variable to specify location of the FSL), just Suggest
> >  fsl-core package (can't recommend stuff from non-free)

> Is the libfslio.so that comes with the current FSL-package compiled in a way that it can be loaded at runtime(a module)?

didn't check ;)  but it seems to be it is all fine:

LD_LIBRARY_PATH=/usr/lib/fsl/5.0/ python -c "from ctypes import cdll; l=cdll.LoadLibrary('libfslio.so'); print dir(l); print l.FslSeekVolume"
['_FuncPtr', '__class__', '__delattr__', '__dict__', '__doc__', '__format__', '__getattr__', '__getattribute__', '__getitem__', '__hash__', '__init__', '__module__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', '__weakref__', '_func_flags_', '_func_restype_', '_handle', '_name']
<_FuncPtr object at 0x7feff5153390>

> Other than that I don’t really see a problem in doing so.

> > - we do talk to FSL and NIfTI folks to adopt fslio changes from FSL
> >  codebase into nifticlib and build a system-wide available fslio
> >  library

> I would very much like that - that is if it doesn’t take forever :)

well -- actually third alternative could be you just take those copies of
fslio.{c,h} from FSL and  ship/build them along.  Very suboptimal,  some Debian
people might get concerned, but IMHO nothing in Debian policy forbids it.  You
could even start this way and later on we will figure out the 'ideal' way (e.g.
#2 from above)

-- 
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