HCP FreeSurfer 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 second step of structural image processing is used to perform the following operations:

  • spline interpolated downsample to 1 mm

  • initial recon-all step 1

  • initial recon-all step 2

  • initial recon-all step 3

  • high-resolution white matter and fine tuning T2w to T1w registration

  • intermediate recon-all

  • high-resolution pial tuning

  • final recon-all

Within QuNex the HCP pipeline is run using the hcp_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_freesurfer.