dicom COL,ROW vs nifti ROW,COL about dcmstack HOT 3 CLOSED

sorry about close/open. mouse finger slipped.

from dcmstack.

The axis swap is definitely handled. Perhaps you are confusing the voxel data ordering (how the 3D voxel data is stored) versus the orientation in patient space (specified with the affine). You can control the voxel data ordering with the --voxel-order option.

One relatively easy way to check is to look at the results in fslview and make sure that the orientation labels (LRAPSI) match. The way the three orthogonal images are displayed will only match if the voxel data ordering is the same, but the labels will show if the affine is correct. I hope this makes sense.

If you are still convinced there is a problem, perhaps you can share the dataset?

from dcmstack.

You were right, I was confusing voxel data ordering and orientation in patient space. Specifying the voxel order when using DicomStack.to_nifti_wrapper() fixed my problem.

Thank you very much!

from dcmstack.