[MINC-users] NifTi <-> MINC ?

[Christopher Bailey]

Hi,

The lack of much "pure" nifti data is probably due to not-that-many
dicom2nifti converters out there. A quick Google only produced

www.fmrib.ox.ac.uk/~robson/internal/Dicom2Nifti.htm

FSL, for example, can read and write both analyze and nifti. By default,
anything it's functions/programs write out will be gzipped nifti format.
You can be cheaky and do

avwmaths input.hdr -mul 1 output.nii.gz

to get a nifti "copy" of an analyze file. This will only work in FSL >
3.2 beta.

-Chris


On Thu, 2004-12-09 at 14:45, Robert VINCENT wrote:
> Hi all,
> 
> I've already written a prototype of this converter for inclusion in the
> next revision of MINC.  So far it only works in one direction (MINC ->
> NIfTI-1).  I'd appreciate any test data that you can provide, my main
> delay has been a lack of decent NIfTI-1 examples.
> 
> 	-bert
> 
> On Thu, 9 Dec 2004, Morgan Hough wrote:
> 
> > Sorry. Good point. I have added information about the files to the
> > webpage (http://www.fmrib.ox.ac.uk/~mhough/data.html) as well as a
> > functional dataset.
> >
> > Hope this is useful.
> >
> > Cheers,
> >
> > -Morgan
> >
> > --
> > Morgan Hough  DPhil student
> > FMRIB, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> > mhough@fmrib.ox.ac.uk  www.fmrib.ox.ac.uk/~mhough
> > tel +44 (0) 1865 222545  fax +44 (0) 1865 222717
> >
> > On Thu, 2004-12-09 at 11:49, Christopher Bailey wrote:
> > > Thought so!
> > >
> > > I see Morgan has already provided some example data. Perhaps the details
> > > of the file (dimensions, steps, etc) would be handy when testing a
> > > converter. Morgan?
> > >
> > > As a caveat emptor to what I said previously, the next two paragraphs
> > > are by Mark Jenkinson on the FSL mailing list:
> > >
> > > "
> > > The current FSL release is a beta release and we have
> > > not yet taken advantage of the full set of possibilities that
> > > the nifti file format creates.  Part of this is that we do not
> > > use qforms in any of our processing at present.  We do
> > > use sforms for calculating standard space coordinates,
> > > as is implemented in the current version of fslview.
> > >
> > > Therefore, at present all fsl routines work in ijk coordinates
> > > in the same way that they always have before.  As Dave says,
> > > the next version of fsl will be likely to support qforms.
> > > "
> > >
> > > So for some time to come we should be aware that the full NifTi
> > > specification is not used by FSL programs (SPM?).
> > >
> > > -Chris (volunteer beta tester)
> > >
> > > On Thu, 2004-12-09 at 11:47, Andrew Janke wrote:
> > > > On Thu, 9 Dec 2004, Christopher Bailey wrote:
> > > >
> > > > > Dear list (not to mention Andrew ;),
> > > > >
> > > > > Has anyone out there written a NifTi <-> MINC converter? With the new
> > > > > analyze replacement, there's some hope of L-R consistency etc. when
> > > > > converting to/from MINC. I still vow to lobby inclusion of MINC I/O in
> > > > > FSL, but until that happens, I'm stuck with converting.
> > > > >
> > > > > Just wanted to hear if anyone had already put effort into this
> > > > > (re-inventing the wheel, and all that...).
> > > >
> > > > Guilty as charged.  I have begun some initial work on adding another analyze
> > > > "type" to ana2mnc but haven't released anyhting yet. If only because I am yet to
> > > > see some example NIFTI-1 files.  So if you have some and can put them on a
> > > > download site somewhere I'll then have something to test what I have with!
> > > >
> > > > My current approach was to wait untill someone asked for it and then worry about
> > > > it.  And now someone has..... :)
> > > >
> > > >
> > > >
> > > > --
> > > > Andrew Janke (andrew_janke@iinet.net DOT au || www.cmr.uq.edu.au/~rotor)
> > > > Australia->Brisbane            H: +61 7 3390 6332  || M: +61 4 2138 8581
> > >
> > > _______________________________________________
> > > MINC-users@bic.mni.mcgill.ca
> > > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> >
> > _______________________________________________
> > MINC-users@bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> 
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