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ENHANCE-PET / MOOSE

MOOSE (Multi-organ objective segmentation) a data-centric AI solution that generates multilabel organ segmentations to facilitate systemic TB whole-person research.The pipeline is based on nn-UNet and has the capability to segment 120 unique tissue classes from a whole-body 18F-FDG PET/CT image.
https://enhance.pet
GNU General Public License v3.0
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Brain cropping fails with dynamic datasets #38

Closed DariaFerrara closed 2 years ago

DariaFerrara commented 2 years ago

The following error occurred after using Moose with dynamic datasets of Vision lung cancer patients. All other segmentations and SUV extraction properly worked. No error occurred after re-running Moose with the corresponding static dataset. 

Brain found in field-of-view of PET/CT data...                         
- Cropping brain from PET image using the aligned CT brain mask
Traceback (most recent call last):
  File "/usr/local/bin/moose", line 215, in <module>
    cropped_pet_brain = iop.crop_image_using_mask(image_to_crop=pet_file[0],
  File "/home/mz/Documents/Softwares/MOOSE/src/imageOp.py", line 237, in crop_image_using_mask
    out_of_bounds = upper_bounds >= img_dim
ValueError: operands could not be broadcast together with shapes (3,) (4,)
Keyn34 commented 2 years ago

It looks like the error occurs due to the dimension mismatch with the PET image. Just discarding the fourth dimension should resolve that issue if 4D data is a legit input for MOOSE.

LalithShiyam commented 2 years ago

Guys, this is a duplicate issue. Closing it. Refer the previous issue here: https://github.com/QIMP-Team/MOOSE/issues/30. The new version was never built for dynamic PET. And I am not planning to implement it anytime soon.