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Transformations
Bridging transformations are named with a prefix of the form: TARGET_SOURCE, where TARGET is the name of one template space, and SOURCE is the name of another [1]. This transform:
- maps point coordinates in
TARGETspace toSOURCEspace. - Is used to transform images in
SOURCEspace toTARGETspace.
[1] Following the convention set forth in the NeuroAnatomy Toolbox's bridging registrations.
Deformable registration with ANTs for TARGET and SOURCE generates output three output files, an "Affine" file, a "Warp" file, and an "InverseWarp" file.
This library provides several scripts for applying spatial transformations to images or points / skeletons.
When possible, use ANTs' WarpImageMultiTransform, antsApplyTransforms, or CMTK's reformatx to apply transformations generated by ANTs and CMTK, respectively.
In other cases, the script renderTransformed may be helpful.
The R package nat has great tools for analyzing skeletons, including transforming them with CMTK-compatible transformations. For other transforms, see below for scripts that convert transforms to CMTK-compatible formats.
Use the script transformSwc to transform skeletons stored as swc files.
When possible, use ANTs' antsApplyTransformsToPoints, or CMTK's streamxform to transform points.
In other cases, the script transformPoints may be helpful in transforming arbitrary points and point-lists.
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.