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Neuroanatomical Segmentation 2020

Key Investigators

Project Description

  1. The objective of this project is to establish tools and techniques to produce a high resolution manual segmentation of the human brain.


  1. Integrate Freesurfer file formats.
    Freesurfer is a program used to generate brain surfaces from MRI data. Freesurfer file formats use their own coordinate space and thus do not seamlessly integrate with the MRI files read by Slicer. The objective is to make freesurfer file formats easily accessible within Slicer.
  2. Sulcal Drawing The use of 3D tools to draw and delimit brain sulci depends on freesurfer input (number 1) and an algorithm to draw on sulci and extract the lines in coordinate space. The goal is to troubleshoot this process.
  3. Case Management
    • Integration of a BIDS-based cased management system would aid organization and segmentation.
    • Version Control for segmentation

Approach and Plan

  1. Freesurfer integration
    • Load freesurfer surfaces into Slicer
  2. Sulcal Drawing
    • Using the white matter surfaces, draw two points in Slicer, each at the base of a sulcus
    • Connect the two points with a line at the bottom of the sulcus (i.e., a minimum value)
    • Assign the line to a specific sulcal identity.
    • Implement a constraint option for markups to force them to be on a surface (i.e. model node, segmentation, or another markup)
  3. Case Management
    • Pilot organization
    • Add git PR management tools to Slicer module.
      • While editing, save and commit changes to local branch
      • Push changes to branch on Git
      • When completed, create PR for review
    • Segment diff tool
    • Review by interating through the slices and adding comments to a table
    • Keep last two segmentation versions (reviewer + author) for comparison.

Progress and Next Steps

  1. Freesurfer integration
    • Implemented an extension (SlicerFreeSurferImporter) that can import surfaces from FreeSurfer in the correct coordinate system) 2. 3.
  2. Segment Diff Module
    • Implement a module that can calculate and display differences between segments


Background and References