[SciPy-dev] Nifti support

John Ollinger ollinger@wisc....
Thu Oct 4 14:35:39 CDT 2007


I would like to put in my two-cents worth regarding the nifti format.  I
wrote a library in python that handles dicom, afni, and nifti format with
the appropriate conversions between coordinate systems.  The goal was to be
able to script FSL, AFNI, SPM and our in-house python code without doing a
file conversion at every step.  Unfortunately,  AFNI defines the quaternion
transformation relative to LPI coordinates, while FSL defines it as going to
RAI.  I don't know how SPM does it - we are still in the process of
scripting that.   The result is that either the fans of fslview or the fans
of AFNI are upset about any given solution.

I don't know if this is covered elsewhere or not, but it should receive some
attention.

John

p.s. I would contribute the code if anyone is interested.  I completely
rewrote the mess that I offered last spring, and it is probably respectable
python code now although it could stand being refactored again.


On 10/1/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
>
> Excellent news !!
>
> Matthieu
>
> 2007/10/1, Jarrod Millman <millman@berkeley.edu>:
> >
> > On 9/30/07, Matthieu Brucher <matthieu.brucher@gmail.com> wrote:
> > > I saw that nifti file support was currently in the pipeline. If the
> > license
> > > issue is solved, I can provide you a nifticlib.i file that is
> > compatible
> > > with C89 compilers (the converted file needs a C99 compiler, so
> > compiling it
> > > with MSVC is not possible), as I've done this for my hobbies some
> > weeks ago.
> >
> > Hey Matthieu,
> >
> > The pynifti license issue has been resolved.  Michael Hanke, the
> > author, has released his software under an MIT license:
> >
> > http://sourceforge.net/project/shownotes.php?group_id=126549&release_id=543252
> >
> > Early this week, Chris Burns and I will check this code into the SciPy
> > repository.  Once we do, it would be great if you could either
> > integrate your nifticlib.i into the codebase or just send us your
> > code.
> >
> > Thanks,
> >
> > --
> > Jarrod Millman
> > Computational Infrastructure for Research Labs
> > 10 Giannini Hall, UC Berkeley
> > phone: 510.643.4014
> > http://cirl.berkeley.edu/
> > _______________________________________________
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> > Scipy-dev@scipy.org
> > http://projects.scipy.org/mailman/listinfo/scipy-dev
> >
>
>
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-- 
John Ollinger
University of Wisconsin
Waisman Center, T233
1500 Highland Ave
Madison, WI 53711
http://brainimaging.waisman.wisc.edu/~jjo/
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