Incorrect dimension order with HDF5 warp field transforms
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- Dominant language
- Python
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- 35
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- Avg merge
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Description
Hello,
It seems that loading composite transforms using ITKCompositeH5 may generate incorrect warp fields data. Here is some minimal code and data to replicate the problem:
https://www.dropbox.com/sh/9q7fkiil5acd9wy/AAD9IAK-fPIQZ6HSke67nFPea?dl=0
My understanding is that the tensor dimensions were messed up when the warp field data was loaded from the HDF5 file, somehow the first and the third dimensions were swapped.
ants_t1_to_mniComposite.h5 was from a working directory of fMRIPrep 21.0.2, and it's identical to sub-*_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5 in the output directory. The NIFTI file was generated using CompositeTransformUtil --disassemble ants_t1_to_mniComposite.h5 ants_t1_to_mniComposite.
Best,
Feilong
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First steps
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Research direction
Start by reproducing the issue with the linked data and ants_t1_to_mniComposite.h5, using ITKCompositeH5 and the NIFTI produced by CompositeTransformUtil --disassemble. Trace how the composite transform loads the warp field and verify the tensor dimension order; done means the loaded warp field matches the expected NIFTI orientation without swapping the first and third dimensions.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- computer-vision
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100