DICOM to NIFTI conversion

[rickychen]

Operating system: Windows 10
Slicer version: 4.10.2

Hi guys,

I’m wondering if someone knows how Slicer deals with the DICOM to NIFTI conversion? More specifically, what packages or tools do they use to achieve this? Is there any source code online on Slicer repo?

I know in Slicer, the DICOM file can be loaded into the scene and saved as various formats like .nrrd or NIFTI.

Best regards,
Ricky

[Sam_Horvath (Sam Horvath (Kitware))]

Slicer loads from DICOM into its internal representation (vtkImageData) using a number of libraries. mostly GDCM and DCMTK. It then uses ITK file writers to create the NIFTI image.

[pieper (Steve Pieper (Isomics, Inc.))]

@rickychen

More specifically, what packages or tools do they use to achieve this? Is there any source code online on Slicer repo?

The code with DICOM in the name here is a place to start, but this code itself relies on multiple libraries:

Also this thread may help you:

How to convert dicom files to nrrd

You can also consider one of the many tools out there that are much easier to use than Slicer for batch volume reconstruction (faster, easier to use, possibly more robust). You can find a list of some of the most popular ones (incomplete, I am sure) here: https://na-mic.github.io/ProjectWeek/PW27_2018_Boston/Projects/DICOMVolumeReconstruction/. A number of them (including Slicer converters) are set up in this dockerfile: https://github.com/QIICR/dcmheat/blob/master/docker/Dockerfile (just noti…