@m113r encountered rotated geometries in his images. Currently they do not work without resampling for ROIs as those are restricted to non-rotated geometries.
Hence, in version 2 of the MITK ROI file format, it should be possible to define Geometries by affine transforms as an alternative to origin and spacing. I suggest a 16 element JSON array called "Transform" that contains the 4x4 matrix of an affine transform.
Reminder:
d11 d21 d31 0 d12 d22 d32 0 d13 d23 d33 0 t1 t2 t3 1
Where d1, d2, and d3 are the space direction columns, each implicitly defining the spacing and together defining the 3x3 rotation matrix, and t is the translation/offset/origin vector.
So, for example, the transform of Pic3D with origin (0, 0, 0), spacing (1, 1, 3), and image size 256x256x49 is:
1 0 0 0 0 1 0 0 0 0 3 0 0 0 0 1
Which translates to the following JSON:
"Geometry": { "Size": [ 256, 256, 49 ], "Transform": [ 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 3, 0, 0, 0, 0, 1 ] }