DatasetSummary Min and Max on image foreground

[NabJa]

Hello MONAI community,

In the DatasetSummary class the min and max voxel intensities are computed on the whole image (here).
However, in the nnUNet implementation of the DatasetAnalyzer does extract min and max voxel intensities (here) only on the foreground (see foreground extraction).

Shouldn't the min and max extraction of the voxels be moved to after the foreground extraction?

Thanks in advance for your opinions!
Nabil

[wyli]

thanks for the pointer, let me create a ticket on this...

[Nic-Ma]

Hi @dongyang0122 , what do you think about this question? May I know the thoughts when you develop the DatasetSummary?

Thanks in advance.

[dongyang0122]

@Nic-Ma sorry I have no clue about DatasetSummary

[dongyang0122]

Yes, we need intensity stats on foreground regions. But we need more than that. For example, a common practice is using 5% and 95% of overall intensity distribution as thresholds for intensity clipping.

[yiheng-wang-nv]

Hi @dongyang0122 , for percentiles, can you use calculate_percentiles? See: https://github.com/Project-MONAI/MONAI/blob/dev/monai/data/dataset_summary.py#L155

[Nic-Ma]

Sorry I misunderstood this module, it was developed by @yiheng-wang-nv not @dongyang0122 's AutoML module.

Hi @yiheng-wang-nv , could you please help share some comments? Or maybe you can enhance the features?

Thanks in advance.

[yiheng-wang-nv]

Hi @NabJa , thanks! Let me submit a PR to modify it.