Pre-processing with hippunfold

Hippocampal feature post-processing with z-brains relies heavily on hippunfold, an openly available hippocampal segmentation tool that models the topological folding structure of this region.

The Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a widely used directory and file naming convention in brain imaging. To run hippunfold, and subsequently z-brains, your raw data needs to be conform to BIDS standards.

hippunfold enables surface-based sampling of image intensities and calculation of hippocampal thickness from an input anatomical scan. z-brains subquently uses these surface-mapped for feature smoothing and normalization of available features across participants.

What should I use as an input to hippunfold?

We recommend to use the main structural scan generated by micapipe, i.e. the nativepro T1w scan as input to hippunfold. This way, all generated hippocampal surfaces will be in the same space as other features of interest, which are also co-registered to this space.

Hippocampal thickness

Hippocampal thickness is directly calculated from surfaces generated from inner and outer surfaces output by hippunfold for each participant.

FLAIR, qT1, MD, and FA

Image intensity of available features in your dataset can be sampled along each hippocampal surface. Note that these images should be in the same space as the surfaces generated by hippunfold.