HCP PostFreeSurfer 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 third step of structural image processing is used to perform the following operations:

  • conversion of FreeSurfer volumes and surfaces to NIfTI and CIFTI

  • creation of FreeSurfer ribbon file at full resolution

  • myelin mapping

Within QuNex the HCP pipeline is run using the hcp_post_freesurfer command. Do note that the exact steps that are executed depend on parameters specified. In contrast to the original HCP pipeline, the modified version of the pipeline included in QuNex 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_post_freesurfer.