If the sform is not available (as determined from the sform code),
then SPM will use the contents of the qform to determine the image
orientation. Generating an appropriate matrix from the qform
information is done by @nifti/private/decode_qform0.m .
All the best,
-John
On 23 July 2012 21:47, Neggers, S.F.W. <[log in to unmask]> wrote:
> Dear SPMers,
>
> a question for you fellow nii coders (and somehow I feel John is going to answer this one). When you are not interested in the depths of nii file header encoding and specs please stop reading here, this is really boring stuff.
>
> SPM seems to prefer working with voxel to world mappings as encoded in the srow matrix of the formal nifti file header specification (http://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h ), especially the srow_x, srow_y and srow_z vectors. When a nii image has this srow information, this is signalled in the header with the bit sform_code set to 1. So far so good.
>
> I have nii data now from some scanner where space is only encoded as a quaternion (the other way in the nifti header for defining the space of all voxels in the image), and hence the sform_code bit in the nifti header is set to 0, qform_code to 1, and srow is only the unity matrix. Still nifti specs proof, just a bit unusual to me.
>
> SPM seems to display this image well, and a voxel to world matrix is displayed in the graphics window. How exactly does SPM compute the srow matrix from the quaternion? Does it then subsequently use sform_code=1 and the computed srow matrix for subsequent processed data? The nifti website from NIH does offer some pointers on conversions of quaternions, but not a complete description unfortunately.
>
> I need to know as some of my own rendering code doesnt handle that specific data well, it assumes sform_code is always on and the srow fields populated (as it is for SPM data).
>
> Thanks for your insights John (or others),
>
> Bas
>
>
>
> --------------------------------------------------
> Dr. S.F.W. Neggers
> Division of Brain Research
> Rudolf Magnus Institute for Neuroscience
> Utrecht University Medical Center
>
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> : http://www.brainsciencetools.com (CEO)
> --------------------------------------------------
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