HCP PreFreeSurfer pipeline#

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.

The initial step of structural image processing is used to perform the following operations on T1w and T2w high resolution images:

  • gradient distortion correction,

  • averaging of the same files (if multiple scans of the same modality exist),

  • AC-PC alignment,

  • image FNIRT based brain extraction,

  • T2w to T1w image registration,

  • readout distortion correction (optional),

  • bias field correction (optional),

  • linear and non-linear atlas registration to MNI152.

Within QuNex the HCP pipeline is run using the hcp_pre_freesurfer command. Do note that the exact steps that are executed depend on parameters specified and the processing mode requested (e.g. the 'LegacyStyleData') does not require the presence of a T2w image or field maps).

The full list of command's parameters along with example calls can be found at hcp_pre_freesurfer.