/hippocampal_perfusion

Primary LanguageHTML

DOI

Hippocampal perfusion

This repository contains the data analysis code and (visualization) notebooks related to the paper:

"Insights into hippocampal perfusion using high-resolution, multi-modal 7T MRI"

that can be found here.

  • The analysis pipeline (see workflow for more details) is build using the Snakemake workflow management system.
  • Several notebooks are uploaded to support the inspection of the intermediate analysis steps (i.e., hippocampal segmentation and vasculature), as well as the different visualization steps (in visualization).
  • results/surface_maps contains group-averaged surface maps as displayed in the manuscript figures.
  • A more interactive visualization tool of the results is possible using our online data explorer that can be accessed here.

Hippocampal Data Explorer

Dependencies

  • Singularity and containers (see config/config.yml)
  • A virtual environment is recommended with the following packages installed:

Note Raw imaging data, manual segmentations as well as the related code for the image preprocessing steps will be uploaded to a separate data repository after the data manuscript has been accepted for publication.