Diffusion weighted imaging (DWI) 'legacy' data preprocessing#


For all HCP pipeline steps please refer to Running the HCP pipeline. For an overview on how to prepare data and run the HCP preprocessing steps, see Overview of steps for running the HCP pipeline.


Prior to DWI analyses, DWI data must be preprocessed. For multi-shell phase-encoding reversed DWI data please refer to the HCP preprocessing via QuNex.

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 dwi_legacy_gpu command.

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.


  • dwi_legacy_gpu can be run after completion of the hcp_pre_freesurfer command, and may be run before FreeSurfer (see instructions here for HCP preprocessing via QuNex).

  • 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.