You can try our dicom->nifti converter also (lcni.uoregon.edu/~jolinda/MRIConvert). If the results from that seem off, please let me know and I will look into the problem.
--
Jolinda Smith
Lewis Center for Neuroimaging
University of Oregon
Eugene, OR 97403
[log in to unmask]
On Tue, 28 Nov 2006 13:58:14 +0000, Ged Ridgway <[log in to unmask]> wrote:
> Hi,
>
> First off, sorry about my misinterpretation of how you were converting
> from DICOM!
>
> > - Posterior to Anterior is pixel coordinate flipped from Analyze to Nifti
>
> I think this is more likely to be a peculiarity of Analyze than a
> mistake in the NIfTI... see e.g. the rather complicated hist.orient
> field discussed here:
>
> http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm
>
> > - Physical coordinates are offset between analyze and nifti
>
> I agree with Mark that the nifti origin looks suspiciously far away
> from the image centre. There doesn't seem to be any obvious
> relationship between the Analyze origin and the nifti qform's 4th
> column...
>
> > - The nifti coordinates show that the Y and the Z axes are coupled
> > (i.e. z changes if I change y and vice versa).
> > I didn't expect this and if Y is coupled to Z, I would expect X to
> > be coupled also (it's not).
>
> This however, isn't necessarily wrong, in my opinion. This coupling
> between the Y and Z axes (but not the X axis) simply results from a
> small rotation around the X axis. This is also what the qform below
> encodes.
>
> > qto_xyz:1 -3.281250 0.000000 -0.000000 638.135620
> > qto_xyz:2 0.000000 -3.275130 -0.305243 644.623718
> > qto_xyz:3 -0.000000 -0.200316 4.990674 11.303008
> > qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>
> It could simply be that the debabeler is taking into account a
> rotation specified by the DICOM direction cosines that SPM2's Analyze
> conversion ignores (because Analyze wouldn't be able to properly
> handle this anyway). Likewise, it seems possible to me that the NIfTI
> origin could be correctly set from the (peculiar) origin in the
> DICOMs. Although it does look odd...
>
> I guess the best thing to do would be to try some other DICOM->NIfTI
> conversion tools and see how they compare. If you're very keen, you
> could investigate the DICOMs directly, but it can get rather confusing...
>
> Best,
> Ged.
>
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