Mapping HCP pipeline results to QuNex file hierarchy organization#


For an overview on how to prepare data and run the HCP preprocessing steps, see Overview of steps for running the HCP pipeline.

Once images are preprocessed using HCP pipelines, the results need to be mapped back to the QuNex folder structure. This step is accomplished using map_hcp_data command. The command uses information from the batch file and does the following:

  • maps high resolution T1w image

  • maps high resolution FreeSurfer aparc+aseg segmentation

  • creates low resolution version (matching BOLD images) of FreeSurfer aparc+aseg segmentation

  • maps 32k low resolution surface maps and generates an updated .spec file

  • maps volume and grayordinate (CIFTI) BOLD images

  • generates a movement correction report file

Parameters that are relevant for this step and should be set either in the command line or in a batch.txt file. They can be found in the map_hcp_data command's online reference.