Steve Pieper

This command line successfully converts one NSCLC-Radiomics study downloaded from TCIA to nrrd. ``` /c/Program\ Files/Slicer\ 4.7.0-2017-06-11/Slicer.exe --no-main-window \ --python-script /c/Users/pieper/AppData/Roaming/NA-MIC/Extensions-26083/SlicerRT/lib/Slicer-4.7/qt-scripted-modules/BatchStructureSetConversion.py \ --input-folder ./DOI/LUNG1-001 \ --export-images \ --output-folder /d/data/nsclc-radiomics/converted ```...

Will work on data conversion scripts in [this repository ](https://github.com/pieper/Converters) while prototyping.

@fedorov Yes, something simple is better if it works well. But can it convert the RT Structure Sets?

@fedorov do have you had good luck with dicom2nifti on various sample data? It appears the license is compatible with Slicer and we could consider using it as another approach...

@ihnorton FYI

I didn't look too closely but I think dicom2nifti is pure python, right? On Fri, Jul 7, 2017 at 2:50 PM, Isaiah wrote: > Sorry - it doesn't really work...

@HIBhl with the latest Slicer and SlicerRT (the nightly) structure sets will load as Segmentations and you can export them to Labelmaps that can be saved as nrrd. https://www.slicer.org/wiki/Documentation/Nightly/Modules/Segmentations Also,...

Sounds like you are very close. There are options in the SlicerRT/Segmentations code in slicer to set the reference geometry of the label map, but they aren't in the batch...

I particularly like this line in their readme: > funding — to point to the sources of funding which provided support for a given functionality implementation and/or method development If...

The image looks the same on Slicer as it does on OHIF, so I'd say horos is applying a different window/level for some reason. Slicer reports: ``` Window/level found in...