# HCP fMRIVolume pipeline

````{admonition} Prerequisites
* [HCP PostFreeSurfer](../UsageDocs/HCPPostFreeSurfer)
````

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 fourth step is used to perform the following operations on BOLD image files:

* slice timing correction
* gradient distortion correction
* motion correction
* EPI distortion correction
* registration to T1w image
* one step resampling to target space
* intensity normalization
* bias removal

Within QuNex the HCP pipeline is run using the [`hcp_fmri_volume`](../../api/gmri/hcp_fmri_volume.rst) command. Do note that the exact steps that are run depend on parameters specified. In contrast to the original HCP pipeline, the modified version of the pipeline included in QuNex enables a number of additional or changed options, most of then aimed at enabling and optimizing processing of legacy, single-band images. Specifically, the modified code:

* enables slice timing correction,
* allows execution without reference (scout) BOLD images,
* allows the choice between FLIRT and McFLIRT motion correction,
* allows movement correction and registration to the first BOLD image rather than each BOLD image being independently processed and registered to T1w image,
* in combination with the above it allows perusing EPI distortion correction computed for the first BOLD image or the last image with new spin-echo reference pair,
* it allows optional non-linear registration between BOLD runs when registration between BOLD images is enabled, and
* it extends options for BOLD masking from individual mask based on the individual's T1w image to mask based on BOLD (scout) image, dilated MNI brain mask and no masking.

The full list of command's parameters along with example calls can be found at [`hcp_fmri_volume`](../../api/gmri/hcp_fmri_volume.rst).