matRad
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matRad has issues with 2D patients
For some applications it might be interesting to first evaluate on a 2D phantom. However, matRad has problems when the 3rd dimension is only of size 1 (MATLAB removes the last dimension and thus some array accesses fail, for example sz = size(ct.cube{1}) gives only a 1x2 array, and sz(3) will then lead to a crash.)