Deal with dicom to niftii conversions

[NathanMolinier]

Description

The objective of this issue is to discuss about dicom to niftii and niftii to dicom conversions.

Functions to explore

• https://github.com/qurit/rt-utils
• https://razorx89.github.io/pydicom-seg/guides/write.html
• https://github.com/gacou54/to_dicom_seg

[Nilser3]

I find interesting the approach of rt-utils, especially its facility to save the input in a new array.

But I had issues to keep the orientation of the inputs and outputs (see image).
also, as it is a mesh and not voxels, I observe interpolation problems in very irregular contours.

I will explore pydicom-seg approaches: #2

Orientation issues reported

qurit/rt-utils#102
qurit/rt-utils#84

[NathanMolinier]

Nifti and DICOM are using a different spacial coordinate system

[NathanMolinier]

Very interesting issue about DICOM orientation: https://gist.github.com/agirault/60a72bdaea4a2126ecd08912137fe641