Hi,
I am looking into replacing an ANTs registration step with FreeSurfer SynthMorph for a processing pipeline. FreeSurfer uses RAS orientation while ANTs/ITK uses LPS.
I can successfully get my RAS xfm to LPS with FreeSurfer’s mri_warp_convert -g moving.nii.gz --inras warp.mgz --outlps warp.h5
, but that resultant .H5 file does not have the expected ANTs H5 header, which leads me to the following error when the registration is applied later with antsApplyTransform
:
Description: ITK ERROR: TransformFileReaderTemplate(0x55565df6abb0): Could not create Transform IO object for reading file /home/smeisler/projects/fmriprep_ants/single_subject_bids/derivatives/synthmorph_test/sub-NDARINV1Y40DZT8/ses-baselineYear1Arm1/anat/sub-NDARINV1Y40DZT8_ses-baselineYear1Arm1_rec-normalized_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5
Tried to create one of the following:
HDF5TransformIOTemplate
HDF5TransformIOTemplate
MINCTransformIOTemplate
MINCTransformIOTemplate
MatlabTransformIOTemplate
MatlabTransformIOTemplate
TxtTransformIOTemplate
TxtTransformIOTemplate
You probably failed to set a file suffix, or
set the suffix to an unsupported type.
Unfortunately, I need to keep the xfm to be an .h5 file, or at least I would like to (otherwise I’ll have to tinker with more of the pipeline than I had anticipated).
So the main question is: Is there a utility that can add ANTs header information to a transform file such that antsApplyRegistration
will behave better?
Thanks,
Steven