Fix radiomics features units

[vkt1414]

This PR addresses #33 and thanks for catching the error.

Summary: Added Hounsfield Unit as the unit for all intensity fields based on IBSI documentation.

Here was my understanding upon reading IBSI paper. https://pubs.rsna.org/doi/suppl/10.1148/radiol.2020191145/suppl_file/IBSI_Reference_Manual.pdf

We must use calibrated units for CT and for modalities like MRI we must use arbitrary units a/c below paragraph from IBSI. Examples of calibrated units were Hounsfield for CT and SUV for PET

That means we must use Intensity-based statistical features to encode all intensity-based radiomics features for modalities like CT and Intensity histogram features for modalities like MRI.

However, there are two features that pyradomics refers to Intensity histogram features by default,

• Entropy
• Uniformity

For units, this was my thought process, Wherever Xgl is present, I assumed the unit will be Hounsfield Unit and X^2 will be square Hounsfield Unit. While I could find Hounsfield Unit as [hnsf'U], I presumed, square Hounsfield Unit as [hnsf'U]2 but we may need to confirm it with D.Clunie.

It would be great to have a second set of eyes to confirm that the units are correct, as this seems to be vulnerable to errors.

[vkt1414]

Just one small fix is needed, unless I messed it up - looks good otherwise!

Thank you! I corrected the units now.

[fedorov]

To follow up on the above, it seems that pyradiomics will always calculate statistical minimum/maximum (see https://github.com/AIM-Harvard/pyradiomics/blob/master/radiomics/firstorder.py#L71-L95), without binning. Which means we should use IBSI code 1GSF (see below).

However, the standard appears to only contain codes for discretized intensity 1PR8:

See in part 16: https://dicom.nema.org/medical/dicom/current/output/chtml/part16/sect_cid_7478.html.

@dclunie why is the first type of intensity feature with code 1GSF is not included in the standard?

[fedorov]

@vkt1414 we discussed the above with @dclunie and confirmed we should use the appropriate code from IBSI even if it is not included in the standard. David will amend the standard to include missing codes.

[fedorov]

@dclunie to follow up on what you said: what are the DICOM means to know the input units of pixel intensity other than Modality for CT?

[fedorov]

Per discussion, for now we will abort the workflow if the input is not CT, but for the reference, here are some comments from @dclunie:

• RescaleType https://dicom.innolitics.com/ciods/ct-image/ct-image/00281054 is intended for communicating units, but looking at our data, it often contains invalid information

DICOM CT images are HU unless otherwise specified:

https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.2.html#para_ac9aacea-a51a-40d4-8398-77d8b09cfd9a

and for multi-energy CT it has become complicated:

https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.11.html#sect_C.11.1.1.2

There is also PET, which has an attribute called Units:

https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.9.html#sect_C.8.9.1.1.3