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Overview of steps for running the HCP pipeline


As noted, the QuNex Suite implements the HCP pipelines. It introduces and makes use of the modifications that allow processing of both multi-band HCP-compliant data ('HCPStyleData' processing mode) as well as 'legacy' data ('LegacyStyleData' processing mode), which allows preprocessing of imaging data that does not conform to all the imaging standards required by the HCPpipelines. Specifically, it enables preprocessing of 'legacy', single-band BOLD and DWI data, with coarser resolution, longer TRs, and data that is missing field maps and/or a high-resolution T2w image. Of note, using legacy style data will yield inferior results by definition. The user should always attempt to collect data that meets full HCP specifications when starting new data collection.

Preprocessing is implemented in three general steps:

See the linked pages where these three steps and the relevant commands are described in more detail.