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, minc-toolkit and MNI priors. The pipeline is contstructed in a modular manner using the bpipe pipelining tool, enabling parallel processing of subjects and integration with clusters if available. minc-bpipe-library performs the steps of bias field correction, image registration[1,2], masking and brain extraction, 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.
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