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mist-medical / MIST

MIST: A simple, scalable, and end-to-end framework for 3D medical imaging segmentation.
Apache License 2.0
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bound box altered #22

Closed fuentesdt closed 5 months ago

fuentesdt commented 6 months ago

The bounding box of the output segmentation is altered from the original image. This causes downstream problems with packages like pyradiomics

$ c3d Art.raw.nii.gz -info Art.liver.nii.gz -info Image #1: dim = [320, 258, 88]; bb = {[-197.665 -169.311 -96.9695], [222.335 169.314 167.03]}; vox = [1.3125, 1.3125, 3]; range = [0, 543]; orient = Oblique, closest to RAI

Image #2: dim = [320, 258, 88]; bb = {[-201.603 -188.998 -96.9766], [218.397 149.627 167.023]}; vox = [1.3125, 1.3125, 3]; range = [0, 1]; orient = Oblique, closest to RAI

aecelaya commented 6 months ago

Can you try the -mbb flag with c3d?

c3d reference.nii target.nii -mbb -o out.nii

aecelaya commented 5 months ago

The latest release should address this issue. Let me know if it persists.