WIP(convert tool to transform)-135 add DICOM loader

[Nic-Ma]

Fixes #135 .

Description

This PR implemented a medical image format converter.
Convert medical image formats with option to resample image.
Supported input formats: .dcm, .nii, .nii.gz, .mha, .mhd.
Supported output formats: .nii, .nii.gz, .mha, .mhd.

Status

Ready

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• Breaking change (fix or new feature that would cause existing functionality to change)
• New tests added to cover the changes
• Docstrings/Documentation updated

[aylward]

I don't recommend creating dependencies on SimpleITK. Consider using the full ITK - pip install itk

[aylward]

See comments regarding SITK versus ITK.

ITK provides pipelining (data streaming, parallelism, etc), meshes, the ability to explicit specify template parameters of a filter, interfaces with numpy, and access to remote modules - ITK is the way to go.

You may also want to consider ITKWidgets for image, mesh, ... visualization in jupyter notebooks/labs:
https://github.com/InsightSoftwareConsortium/itkwidgets

[Nic-Ma]

Hi All,

I updated the code to be compatible with master.
Could you please help review it again?
Thanks.

[wyli]

i think we need to have a loader wrapped as a transform, to show the idea that monai doesn't implement its own but build wrapper around external packages for this type of IO tasks. provide a CLI script is not proper integration... as a starting point let's use pydicom

[zsdqui]

any update on this WIP? Any thoughts on adding support for dicom-RT. Being able to load RT-struct files would greatly assist utilizing MONAI for radiotherapy applications.

[Nic-Ma]

any update on this WIP? Any thoughts on adding support for dicom-RT. Being able to load RT-struct files would greatly assist utilizing MONAI for radiotherapy applications.

Hi @zsdqui ,

Thanks for your suggestion.
I think our working group is discussing the DICOM support.
Thanks.

[wyli]

this is out-of-date and becomes really confusing, I'm closing it now (the branch will be retained)