Software Tool to Read, Represent, Manipulate, and Apply N-Dimensional Spatial Transforms

Spatial transforms formalize mappings between coordinates of objects in biomedical images. Transforms typically are the outcome of image registration methodologies, which estimate the alignment between two images. Image registration is a prominent task present in nearly all standard image processing and analysis pipelines. The proliferation of software implementations of image registration methodologies has resulted in a spread of data structures and file formats used to preserve and communicate transforms. This segregation of formats hinders the compatibility between tools and endangers the reproducibility of results. We propose a software tool capable of converting between formats and resampling images to apply transforms generated by the most popular neuroimaging packages and libraries (AFNI, FSL, FreeSurfer, ITK, and SPM). The proposed software is subject to continuous integration tests to check the compatibility with each supported tool after every change to the code base (https://github.com/poldracklab/nitransforms). Compatibility between software tools and imaging formats is a necessary bridge to ensure the reproducibility of results and enable the optimization and evaluation of current image processing and analysis workflows.