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Structural and functional asymmetry of the neonatal cerebral cortex

Development of symmetric surface-based atlas

This is a repo containing files and scripts used to investigate cortical asymmetry in the Developing Human Conenctome Project and Human Connectome Project (Young Adult).

Software used for cortical surface processing and analysis

  1. Multimodal surface matching (MSM)
  2. Connectome Workbench
  3. FSL GLM Setup
  4. FSL PALM

Steps for performing analysis

1. Cortical surface registration

First, cortical surfaces need to be registered from their native space to the fully-symmetrised templates contained in ~/metrics-lab/CorticalAsymmetry/Templates. Registration is run using MSM, and is driven by cortical folding.

dHCP: Registration was run using align_to_template_3rd_release.sh. The cortical surface deformations released as part of the 3rd dHCP release are NOT the same as the ones used in this manuscript (a further symmetrisation step was performed after release of the data).

HCP-YA: Registration was run using CorticalSurfaceRegistration.sh

dHCP-to-HCP: Registration was run using CorticalSurfaceRegistration.sh. The dHCP-to-HCP registration deformation can be found here.

2. Cortical surface processing

These scripts perform the following steps:

  1. Calculate cortical surface area using the pial surface
  2. Resample anatomical surfaces and structural cortical metrics from native to symmetric template space
  3. Calculate difference maps (asymmetry index maps for each cortical metric) and smooth

dHCP: Use CorticalSurfaceProcessing.sh

HCP-YA: Use CorticalSurfaceProcessing.sh

dHCP-to-HCP: Use CorticalSurfaceProcessing.sh

Code for processing resting-state fMRI for functional asymmetry analyses in the dHCP is located here.

3. Permutation analyses

The command-line calls to PALM used in these analyses are located in ~/metrics-lab/CorticalAsymmetry/PermutationAnalyses. This also contains a README.md describing the flags and the inputs used.

Citation

If you found this code useful, or have used the dHCP symmetric template for your own work, please cite:

Structural and functional asymmetry of the neonatal cerebral cortex

@article{williams2022structural,
  title={Structural and functional asymmetry of the neonatal cerebral cortex},
  author={Williams, Logan ZJ and Fitzgibbon, Sean P and Bozek, Jelena and Winkler, Anderson M and Dimitrova, Ralica and Poppe, Tanya and Schuh, Andreas and Makropoulos, Antonios and Cupitt, John and O’Muircheartaigh, Jonathan and others},
  journal={bioRxiv},
  year={2022}
}