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Transformations
This library provides several scripts for applying spatial transformations to images or points / skeletons.
Use the script renderTransformed to transform images.
Use the script transformSwc to transform skeletons stored as swc files.
Use the script transformPoints to transform skeletons stored as swc files.
We provide a number of spatial transformations that convert images or points/skeletons from one template space to another.
This library supports transformations created by both the ANTs and CMTK image registration packages as well as several custom formats.
We do not support arbitrary affine transforms written by ANTs - a few different conventions / formats are possible. Rather, convert the affines to homogenious matrix and write plain text file using the ANTs utility: ConvertTransformFile.
We support ANTs displacement fields as gzip-compressed Nifti files.
We do not support arbitrary affine transforms written by CMTK. Rather, convert the affines to homogenious matrix and write plain text file using the CMTK utility: dof2mat
CMTK parametrizes the non-linear part of its spatial transformation with B-Splines, usually stored as a compressed text file. We do not currently support this format directly. However, one can convert from this format to a displacement field using the script: cmtk2DField.
The script antsAffine2Cmtk converts the affine component of an ANTs transform to CMTK's format. antsDfield2Cmtk converts a displacement field generated by ANTs to a nrrd file that CMTK understands.