HCP FreeSurfer pipeline
HCP FreeSurfer 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
high-resolution pial tuning
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.