Implements logic for using the muscle_adipose_tissue model & fixes DICOM reading for pydicom >= 3.0.0#139
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wdika wants to merge 1 commit intoStanfordMIMI:mainfrom
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Implements logic for using the muscle_adipose_tissue model & fixes DICOM reading for pydicom >= 3.0.0#139wdika wants to merge 1 commit intoStanfordMIMI:mainfrom
wdika wants to merge 1 commit intoStanfordMIMI:mainfrom
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Implements logic for using the muscle_adipose_tissue model
This PR allows using the muscle_adipose_tissue model, without the spine segmentation. The muscle_adipose_tissue model uses by default the abCT_v0.0.1 segmentation model instead of the stanford_v0.0.2 segmentation model, used by default by the spine_muscle_adipose_tissue model. Also, proper saving to NifTi format is added for the segmentation mask generated by the muscle_adipose_tissue model, allowing to export it as a volume instead of single-slice h5 files.
Fixes DICOM reading for pydicom >= 3.0.0
This PR also updates the DICOM file reading logic to ensure compatibility with pydicom version 3.0.0 and above.