# HCP PreFreeSurfer pipeline

````{admonition} Prerequisites
* [Preparing data for the HCP pipeline](../UsageDocs/PreparingDataHCP)
````

For all HCP pipeline steps please refer to [Running the HCP pipeline](../UsageDocs/RunningPreprocessHCP). For an overview on how to prepare data and run the HCP preprocessing steps, see [Overview of steps for running the HCP pipeline](../UsageDocs/HCPPreprocessing).

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`](../../api/gmri/hcp_pre_freesurfer.rst) 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`](../../api/gmri/hcp_pre_freesurfer).