Dear Sam,
If you want to see the raw header of a NIfTI file, you can do the following:
N = nifti('bold.nii');
N.hdr
Coregister:Estimate will change the voxel-to-world mapping of the source
image through a call to spm_get_space.m:
https://github.com/spm/spm12/blob/r7487/spm_get_space.m#L42-L43
This will edit the sform/qform fields of the NIfTI header, see:
https://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html
Concerning your, I guess, related question on the FSL mailing list,
remember that the 'Transformation matrix' describes the voxel-to-world
mapping, ie how voxel index coordinates (i,j,k) relate to real world
(e.g. mm) continuous coordinates (x,y,z) so this transformation is
always defined, even on unpreprocessed data.
Best regards,
Guillaume.
On 14/03/2019 20:46, Sam W. wrote:
> Hi,
> When I do coregistration: estimate, what parts of the header are changed? Can I see those changes if I compare the original image with the image with changed header using spm_read_hdr or similar function?
> Thanks,
> Sam
>
--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG
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