Obliquity is lost when running 3dAFNItoMINC.
3dinfo data.oblique3+orig
Dataset File: data.oblique3+orig
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Geometry String: "MATRIX(0.870972,-0.00932,0.152387,-110.297,0.002403,0.871986,0.132623,-102.089,-0.083823,-0.071967,1.587195,-43.8519):256,256,49"
Data Axes Tilt: Oblique (7.254 deg. from plumb)
3dAFNItoMINC data.oblique3+orig
About to run /usr/local/freesurfer/mni/bin/rawtominc .....
-xdircos 1 0 0 -ydircos 0 1 0 -zdircos 0 0 1 .....
Can 3dAFNItoMINC be updated? or changed into a script that calls
nii2mnc which seems to work ok?
Could save some people some heartache.