minc-bpipe-library MINC based T1 bpipe preprocessing pipeline

It is common for differing MRI studies to have widely varying fields of view, orienations and intensity ranges for T1-weighted images. The minc-bpipe-library pipeline provides a clusted-integrated preprocessing pipeline for T1-weighted MR images which attempts to standardize images through the application of ANTs[1], minc-toolkit[2] and MNI priors[3]. The pipeline is contstructed in a modular manner using the bpipe[4] pipelining tool, enabling parallel processing of subjects and integration with clusters if available. minc-bpipe-library performs the steps of bias field correction[5], image registration[1,2], masking and brain extraction[6], and field-of-view cropping in order to provide standardized outputs in: native space, un-resampled lsq6 (rigid) MNI space, and lsq12 MNI space.

These outputs are suitable for further processing by a variety of pipelines such as CIVET, MAGeTbrain or antsMultivariateTemplate builder, or Freesurfer.