ReconstructionSuite

A web-based processing and visualization platform for placing and visualizing intracranial electrodes in subject-specific brain space.

Visualize Freesurfer cortical parcellations and subcortical segmentations in the browser

Input: Subject directory with a directory for MR and CT nifti files Output:

• Freesurfer-processed subject directory
• 3D mesh files containing brain regions and electrodes
• BIDS-compliant electrode coordinates
• Webserver to view and localize electrodes

To run:

• docker-compose up --build
• docker exec -it -e SUBJECT=$SUBJECT preprocessor python3 scripts/1_reconstruction.py
• docker exec -it -e SUBJECT=$SUBJECT mesh_generator bash 1_prep.sh
• docker exec -it -e SUBJECT=$SUBJECT mesh_generator bash 2_brainGenerator.sh
• docker exec -it -e SUBJECT=$SUBJECT preprocessor python3 scripts/2_coregistration.py
• docker exec -it mesh_visualizer npm run start
• docker exec -it -e SUBJECT=$SUBJECT mesh_generator bash 3_electrodeGenerator.sh

Example:

The gLTF binary file format allows for optimized viewing directly in browsers and VR/AR devices.

Dependencies:

• Freesurfer
• Various Brainder scripts for mesh generation
  • Matlab/Octave
• Blender (Freesurfer OBJ to FBX/gLTF)
  • Comes with a python interpreter
• acpcdetect for automatic ac-pc detection

Instructions:

• In the docker-compose.yml file edit the volumes field:
  • path to $SUBJECTS_DIR

electrodes.tsv:

name	x	y	z	size
electrodeGroupA'1	4.52036	61.73	66.4995	1
electrodeGroupA'2	1.85841	63.8435	66.9489	1
electrodeGroupA'3	-2.14716	65.0158	67.3797	1
electrodeGroupB'1	-5.17384	65.0651	68.1047	1

reconstruction.glb:

• Brain
  • Gyri
    • all of the left and right hemisphere aparc regions
  • SubcorticalStructs
    • all of the aseg rois
  • WhiteMatter
    • Left-Cerebral-White-Matter
    • Right-Cerebral-White-Matter
• Electrodes
  • electrodeGroupA
    • electrodeGroupA1

Citing

• Preprocessing

  • https://brainder.org/2012/05/08/importing-freesurfer-subcortical-structures-into-blender/
  • https://brainder.org/research/brain-for-blender/

• Visualization

  • https://github.com/FNNDSC/ami

Version 2.0 viewer

• Written with react/react-three-fiber/drei