Hello AFNI experts,
Apologies if the question has been asked before but I could not find an answer.
I was wondering if there is an easy way to preserve the obliquity with 3dZeroPad/3dAllineate, i.e. if I run 3dZeroPad on a volume with “Data Axes Tilt: Oblique (30.600 deg. from plumb)” the output is “Data Axes Tilt: Plumb”.
The same happens if I register an oblique source to an oblique base, the output is Plumb.
I have run ’ 3drefit -atrfloat IJK_TO_DICOM_REAL ’ in the past if so that after I run -card2oblique with 3dWarp the oblique matrix in the nii volume is preserved, but I don’t know how to proceed when there is padding/rotations being applied.
I appreciate that staying within the AFNI format would avoid the problem, but I need to use the output as nii for subsequent analysis…