OK.


On Mon, Dec 23, 2013 at 2:35 PM, Eleftherios Garyfallidis <
notifications@github.com> wrote:

> In doc/faq.rst:
>
> >
> > -  Registration can be tricky. But this is what usually works for us for normal
> > -  healthy adult subjects. We register the FA (fractional anisotropy) images
> > -  to the FMRIB_FA_1mm template which is in MNI space using ``flirt`` and
> > -  ``fnirt`` from FSL. Then we can apply the warping displacements in any
> > -  other scalar volumes that we have to register that scalar volume into the
> > -  MNI space. We need the corresponding inverse displacements
> > -  to map a tractography into MNI space.
> > +  Image coordinates have positive integer values and represent the centres
> > +  $(i, j, k)$ of the voxels. There is an affine transform (stored in the
> > +  nifti file) that takes the image coordinates and transforms them to
>
> It is not stored as a 4x4 matrix in the nifti. I think it saved as sform
> and qform etc...
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/nipy/dipy/pull/293/files#r8536069>
> .
>