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Excluding voxels with no labels #219

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shmann opened this issue Apr 5, 2022 · 2 comments
Closed

Excluding voxels with no labels #219

shmann opened this issue Apr 5, 2022 · 2 comments
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@shmann
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shmann commented Apr 5, 2022

For transfer learning, jaccard loss decreases while dice scores remain relatively constant, and the resulting model spits out empty predictions. Blocks without labels may be interfering with training--per the AMS paper: "The cubes of the MRI scans that did not contain any meningioma voxels were excluded from the training set."

I would like to modify nobrainer.dataset.get_dataset to include a flag to discard blocks without associated labels. Does this seem reasonable? For example:

if(exclude_no_labels): dataset=dataset.filter(lambda x, y: tf.reduce_max(y) != 0)

@shmann shmann added the question label Apr 5, 2022
@satra
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satra commented Apr 5, 2022

@shmann - i think that would be a good addition. it would have to be limited to dataset generators that map to tensors that have segmentation information.

@hvgazula
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duplicate of #336 and fixed but conflicts with pgan training

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