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Add min_size_in_mm to RemoveSmallObjects transform #7034

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AHarouni opened this issue Sep 22, 2023 · 1 comment · Fixed by #7137
Closed

Add min_size_in_mm to RemoveSmallObjects transform #7034

AHarouni opened this issue Sep 22, 2023 · 1 comment · Fixed by #7137

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@AHarouni
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Describe the solution you'd like
RemoveSmallObjects is a great transform that is very much needed. However its arg is
min_size (int) – objects smaller than this size (in pixel) are removed.
Tumors and organs in medical are measured in mm^3 or CC^3. As radiologist same remove tumors that are smaller than 3 mm

Describe alternatives you've considered
I had to use a transform to resample to 1x1x1 so the pixel count is 1mm^3 remove the tumors then resample back to org size. Instead this should be a simple multiplication as we have the dims actual measurements in the metadata

@wyli
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wyli commented Sep 25, 2023

the min_size can take into account the metatensor.pixdim if it's a MetaTensor before the converting

img_np: np.ndarray
img_np, *_ = convert_data_type(img, np.ndarray)

out_np = morphology.remove_small_objects(img_np, min_size, connectivity)

KumoLiu added a commit to KumoLiu/MONAI that referenced this issue Oct 17, 2023
Signed-off-by: KumoLiu <[email protected]>
wyli pushed a commit that referenced this issue Oct 18, 2023
Fixes #7034.

### Description
Add `in_mm3` in `remove_small_objects`, if `in_mm3=True`, `min_size`
will be divided by pixdim when the image is MetaTensor.

### Types of changes
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Non-breaking change (fix or new feature that would not break
existing functionality).
- [ ] Breaking change (fix or new feature that would cause existing
functionality to change).
- [ ] New tests added to cover the changes.
- [ ] Integration tests passed locally by running `./runtests.sh -f -u
--net --coverage`.
- [ ] Quick tests passed locally by running `./runtests.sh --quick
--unittests --disttests`.
- [ ] In-line docstrings updated.
- [ ] Documentation updated, tested `make html` command in the `docs/`
folder.

---------

Signed-off-by: KumoLiu <[email protected]>
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2 participants