Tutorials

These tutorials reproduce the figures found in the HippoMaps paper (DeKraker et al. 2024 ). They also serve as examples for common analyses, and to showcase ways of using HippoMaps tools.

Morphology:

• Morphology
  • Histology data
  • Ultra-high field MRI data at 7T
  • High-field MRI data at 3T

Histology-MRI-9p4T:

• Histology-MRI-9p4T
  • 0) Map and load volumetric data to surfaces
  • 1) Load, plot, and preprocess all surface data
  • 2) Group average and laminar microstructural profiles
  • 3) Summarize data according to primary gradients

MRI-7T-struct:

• MRI-7T-struct
  • 0) Map and load volumetric data to surfaces
  • 1) Load and plot all surface data
  • 2) Stability between subjects
  • 3) Summarize data according to primary gradients

MRI-3T-rsfMRI:

• MRI-3T-rsfMRI
  • 0) Map rsfMRI data to hippocampal surfaces
  • 1) Intrinsic Timescale of hippocampal rsfMRI
  • 2) Calculate Regional Homogeneity
  • 3) Functional connectivity of the hippocampus to neocortex
  • 4) Check consistency for all measures
  • 5) Gradients of differential hippocampal FC

iEEG:

• iEEG
  • 0) Map data to hippocampal surfaces
  • 1) Load the data and examine attributes
  • 2) Spatial extrapolation
  • 2) Summarize data according to primary gradients

DimReduct:

• Dimensionality-Reduction
  • 1) Load all maps and resample
  • 2) Check for correlations with AP, PD, or subfield organizations
  • 3) Gradient decomposition

MRI-3T-taskfMRI:

• MRI-3T-taskfMRI
  • 0) Map data to hippocampal surface
  • 1) Mnemonic Similarity Task (Pattern Separation)
  • 1.1) GLM fit
  • 1.2) Group-averaging and significance/consistency testing
  • 1.3) Consider neocortical results
  • 1.4) Compare to previously mapped features
  • 2) Episodic Retrieval
  • 2.1) GLM fit
  • 2.2) Group-averaging and significance/consistency testing
  • 2.3) Consider the neocortex
  • 3) Episodic encoding -subsequent memory
  • 3.1) GLM fit
  • 3.2) Group-averaging and significance/consistency testing
  • 3.3) Consider the neocortex

TLE-HC:

• Case control atrophy mapping in temporal lobe epilepsy vs healthy controls (TLE-HC)
  • 1) plot group-averages
  • 2) Examine inter-patient (ipsilateral) consistency
  • 3) Contextualize with other maps