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dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC
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XA61A dicom-enhanced 3-planes localizer stacked in a single volume. #894

Closed bpinsard closed 11 hours ago

bpinsard commented 3 days ago

Describe the bug

3-planes/3-orientation localizer from XA61A are stacked in a single volume.

see https://github.com/nipy/nibabel/issues/1392

To reproduce

dcm2niix -o ./ -d 0 -v 2 ../dicoms/mtl/MRe.1.3.12.2.1107.5.2.63.213014.2024111513211206927679828

Expected behavior

multi-frame enhanced dicoms with non-matching orientation should result in multiple niftis with appropriate affines.

Output log

image (cropping face for "defacing")

Version

Chris Rorden's dcm2niiX version v1.0.20240731 (JP2:OpenJPEG) (JP-LS:CharLS) GCC11.4.0 x86-64 (64-bit Linux)

bpinsard commented 3 days ago

I will try to get phantom data from that site to be shareable.

neurolabusc commented 2 days ago

@bpinsard I can not provide any insights without seeing data. However, here are two thoughts:

  1. I would test the latest commit to the dcm2niix development brnach (v1.0.20241127) which adds several kludges for XA61 data.
  2. I always run dcm2niix with the ignore derived and localizer flag (-i y). Localizers are typically only used for planning and derived data are typically of lower quality than what can be achieved with offline tools. I would have thought that would skip this series entirely.
neurolabusc commented 11 hours ago

As noted here is a limitation of the DICOM data, not dcm2niix. dcm2niix does warn that slice orientation varies, and dcm2niix will ignore these localizer images if the user chooses the -i y option.