Dear FSL team,
I have been trying to register an isotropic (0.8*0.8*0.8 mm3) whole-brain T2-weighted source volume with an anisotropic (0.3*1.2*0.3 mm3) T2-weighted volume covering the brain partially and centred on a region comprising both hippocampi.
To get my registered volume to cover the whole extent of the brain, I produced a nifti reference volume encompassing the target volume as follows:
1) the reference volume has a higher number of voxels than the target volume in each direction
2) the reference volume has the same affine matrix as the target volume, except that it has nonzero values in the fourth (translation) row
Somehow, after I used '-applyxfm -ref [reference volume]' FSL flirt seemed to ignore the translation row and returned a registered volume which was not aligned with the target image.
Is this the expected behaviour? If so, could you please recommend an alternative way to produce a reference that encompasses the target volume?
Thanks for your help,
Alexis
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