A web-based processing and visualization platform for placing and visualizing intracranial electrodes in subject-specific brain space.
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
- 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
The gLTF binary file format allows for optimized viewing directly in browsers and VR/AR devices.
- 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
- In the docker-compose.yml file edit the volumes field:
- path to $SUBJECTS_DIR
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 |
- 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
- Gyri
- Electrodes
- electrodeGroupA
- electrodeGroupA1
- electrodeGroupA
-
Preprocessing
-
Visualization
Version 2.0 viewer
- Written with react/react-three-fiber/drei