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Incorrect dimension order with HDF5 warp field transforms #171

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feilong opened this issue Dec 14, 2022 · 0 comments
Open

Incorrect dimension order with HDF5 warp field transforms #171

feilong opened this issue Dec 14, 2022 · 0 comments

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@feilong
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feilong commented Dec 14, 2022

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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