PyDBS
Deep Brain Stimulation
Parkinson Disease (PD), Essential tremor (ET), Dystonia, but also chronic pain, major depression, Obsessive Compulsive Disorders (OCD)
Deep Brain Stimulation
Parkinson Disease (PD), Essential tremor (ET), Dystonia, but also chronic pain, major depression, Obsessive Compulsive Disorders (OCD)
Major targets for PD: Sub-thalamic nucleus (STN) Globus pallidus interna (Gpi) Ventral Intermediate Thalamic nucleus (VIM)
Deep Brain Stimulation
Parkinson Disease (PD), Essential tremor (ET), Dystonia, but also chronic pain, major depression, Obsessive Compulsive Disorders (OCD)
Major targets for PD: Sub-thalamic nucleus (STN) Globus pallidus interna (Gpi) Ventral Intermediate Thalamic nucleus (VIM)
Major methodological challenges:
Trajectory planning Avoid sulci, vessels, ventricles Optimize electrodes position and direction
The ACouStiC project
www.anr-acoustic.org
Provide to the surgeon patient-specific and generic models
www.anr-acoustic.org
Provide to the surgeon patient-specific and generic models
Automatic target localization and trajectory planning
www.anr-acoustic.org
2. Manual segmentation of structures on the template:
Validation with manual segmentation of 10 patient images
Haegelen C, Jannin P,, Morandi X, Collins L, IJCARS 2012
Models for DBS planning
2. Contacts localization on template
3. Correlation of contacts positions with clinical scores:
1. Motor
2. Neuro-psychological
Lalys, F., Haegelen, C., Abadie, A. (2011). Information Processing in.
Models for DBS planning
Modeling knowledge: surgical rules and constraints
avoid vessels, ventricles etc maximize distance with structures at risk
Maximize alignment with target
Models for DBS planning
Anatomo-clinical atlases
Anatomo-clinical atlases
Anatomo-clinical atlases
Anatomo-clinical atlases
Geometric constraint solver
Models for DBS planning
Anatomical patient-specific model
Import relevant DICOM images
Import relevant DICOM images
Patient Image
dicom nifti
Relational database
Import relevant DICOM images
Patient Image
dicom nifti
Relational database
Import relevant DICOM images
Import relevant DICOM images
Import relevant DICOM images
Import from DB T1 and T2 images
Import from DB T1 and T2 images
Anatomical atlas
Anatomical Segmentation pipeline
Anatomical Segmentation pipeline
Anatomical atlas
T1 → T2 registrationT1 → T2 registration
3D scene generation3D scene generation
T1 → Atlas registrationT1 → Atlas registration
Anatomical atlas
Import from DB T1 and T2 images
Import from DB T1 and T2 images
3D scene generation3D scene generation
T1 → Atlas registrationT1 → Atlas registration
Anatomical atlas
Import from DB T1 and T2 images
Import from DB T1 and T2 images
3D scene generation3D scene generation
Anatomical atlas
Import from DB T1 and T2 images
Import from DB T1 and T2 images
Anatomical atlas
Crop ROICrop ROI
ROI → ROI Non-linearROI → ROI Non-linear
T1 → Atlas registration
0 1 2
Crop ROICrop ROI
ROI → ROI Non-linearROI → ROI Non-linear
T1 → Atlas registration
0 1 2
Crop ROICrop ROI
ROI → ROI Non-linearROI → ROI Non-linear
T1 → Atlas registration
0 1 2
Crop ROICrop ROI
ROI → ROI Non-linearROI → ROI Non-linear
T1 → Atlas registration
Crop ROICrop ROI
ROI → ROI Non-linearROI → ROI Non-linear
0 1 2
3 4 5
Apply inverse transformation
Apply inverse transformation
Skull segmentationSkull segmentation
Frame detectionFrame detection
Stereotactic fame
Stereotactic fame
Pre-Op pipeline
Skull segmentationSkull segmentation
Pre-Op pipeline
Skull segmentationSkull segmentation
Frame detectionFrame detection
Pre-Op pipeline
Skull segmentationSkull segmentation
Frame detectionFrame detection
Stereotactic fame
T1→ AC-PC
Frame detection
Detect frame artifactsDetect frame artifacts Artifacts as ROIs for Frame → CT registration
Artifacts as ROIs for Frame → CT registration
Post-Op pipeline
Electrode model
Cortex masks
CT Pre-Op→ AC-PC
Electrode model
Cortex masks
Electrode detectionElectrode detection
Segmented electrodes
Post-Op pipeline
Pre-Op CT → Post-Op CT registrationElectrode model
Cortex masks
Segmented electrodes
Post-Op pipeline
Electrode detectionElectrode detection
Segmented electrodes
Post-Op pipeline
Electrode detectionElectrode detection
Electrode model
Cortex masks
Segment electrodeSegment electrode
Register electrode model
Register electrode model
Segment electrodeSegment electrode
1 221 22
Register electrode model
Register electrode model
Segment electrodeSegment electrode
Register electrode model
Register electrode model
NIfTI
Implementation
Python
Numpy
NIfTI
Implementation
Python
Numpy
NIfTI
PyDBS
Conclusion
Integrated and fully automated processing pipeline
PyDBS
Conclusion
Integrated and fully automated processing pipeline
Robust when tested on 10 different patients
PyDBS
Conclusion
Integrated and fully automated processing pipeline
Robust when tested on 10 different patients
Relatively fast total processing time < 30 min
PyDBS
Thanks ;)