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SlicerDMRI / SlicerDcm2nii

Support loading DICOM data in Slicer using the functionality of the dcm2niix program.
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DCM2niix failure under slicer #6

Open muratmaga opened 4 years ago

muratmaga commented 4 years ago

I have been trying to fix SlicerDCM2NIix extension to fix the dataset referenced in this thread: https://discourse.slicer.org/t/volume-rendering-produces-block-of-white-noise/10572

I encountered a strange issue. The dcm2niix extension fails under through the SLicer at the final step of conversion (Slicerdcm2nii_error.txt), but works fine if invoked from the command line using the same conversion parameters (dcm2niix_standalone.txt). This on windows 10 (my home computer, I don't have the exact version of slicer, but a preview within the last 1-2 weeks).

dcm2niix_standalone.txt Slicerdcm2nii_error.txt

@lassoan @pieper @fedorov

fedorov commented 4 years ago

@afshinmessiah, is this the same issue that you encountered?

afshinmessiah commented 4 years ago

Yeah, pretty much the same. On slicer, it works for some cases but for the most cases, it does nothing (no error/warning).

pieper commented 4 years ago

@afshinmessiah - do you have a test case that fails consistently? The one @muratmaga pointed to is huge, so it would be good to have a smaller case for testing.

afshinmessiah commented 4 years ago

@piper I looked into it and dug it out a little bit. I guess, I figured the root cause that behavior. The script switches on the -i flag: dcm2niix.exe -i, y, .. which ignores the derived images. Those images which were not opened were derived images and filtered out on slicer. Removing the flag I could open all files. Checked the error for @muratmaga and I think that is a different error (sort of like mixed series due to Slice re-ordering resolved inter-slice distance variability).

pieper commented 4 years ago

Thanks for the update @afshinmessiah.