Diffusion weighted imaging (DWI) 'legacy' data preprocessing
Diffusion weighted imaging (DWI) 'legacy' data preprocessing#
If the DWI data has not been phase-encoding reversed and/or is missing a field map (i.e. pre-HCP 'legacy' acquisitions), then use the
Specifically, this workflow is a modification of
hcp_diffusion that is compatible with 'legacy' data, which have been acquired without a pair of phase-encoding direction reversed images.
dwi_legacy_gpu runs a modified version of the HCP Diffusion preprocessing pipeline, using the "eddy" tool to correct for eddy-current induced field inhomogeneities and head motion, and skipping the "topup" step performed in
hcp_diffusion which would require a pair of phase-encoding reversed images.
At minimum, the pipeline requires a native-space DWI image (single-shell or multi-shell) and a corresponding T1w image, both organized in the standard HCP file hierarchy within the individual session directories (see Data Hierarchy Specification)
For data collected on a Siemens scanner, a standard set of fieldmap images (magnitude and phase) can be used to better correct for field inhomogeneity distortion. However, if fieldmaps are missing the command will omit them.
For detailed instructions on how to use the listed commands, please refer to their online help (by visiting
dwi_legacy_gpu) or embedded help (e.g. by running
qunex dwi_legacy_gpu). For information on other aspects of preprocessing, or for non-legacy DWI data, please consult the HCP preprocessing page.