View source for Project Week 25/Surgical Planning In Stereotaxy

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==Key Investigators==
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* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)


==Project Description==
PyDBS is an automated image processing workflow for planning and postoperative assessment of deep brain stimulation interventions. It takes as input patient-specific data (i.e. patient images and patient clinical data) and generic models (i.e. an anatomical atlas, a model of the stereotactic frame and a model of the implanted electrodes) and provides as output a patient-specific model for planning and postoperative assessment of DBS surgery. This patient-specific model is composed of patient images, segmented anatomical structures (volumetric binary masks and triangular surface meshes) and geometrical transformations (registration matrices and deformation fields). All images, masks and meshes are mapped to a common reference space and fused in geometrical 3D scenes that can be readily visualized by the surgeon.

The software used for visualization and surgical planning is 3D Slicer. PyDBS includes several modules used for targeting and surgery assessment.

{| class="wikitable"
! style="text-align: left; width:27%" |   Objective
! style="text-align: left; width:27%" |   Approach and Plan
! style="text-align: left; width:27%" |   Progress and Next Steps
|- style="vertical-align:top;"
|<!-- Objective bullet points -->
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|<!-- Approach and Plan bullet points -->
* Add new GUI features inspired by the neurosurgeon and neurologist needs
* Add support for multiple trajectories
* Discuss with the core team about how to best include Segmentations in PyDBS

|<!-- Progress and Next steps (fill out at the end of project week), bullet points -->
* Segmentations have been integrated in the core of the toolbox
* GUI has been improved, but there's still some work to do:
** Get inspiration from commercial consoles
** Ask neurosurgeons for feedback
* A [https://github.com/Slicer/Slicer/pull/741 new diverging colormap] has been contributed
|} 

==Illustrations==
[[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
[[File:YeB atlas segmentation.jpg|800px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
[[File:FreeSurfer segmentation epilepsy.png|800px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]
<!--  [[File:Diverging colormap for Jacobian visualization.png|800px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear deformation]] -->
[[File:Jacobian visualization.png|800px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear registration]]

==Background and References==
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* [http://acoustic.univ-rennes1.fr/doku.php/software PyDBS website]
* [https://www.ncbi.nlm.nih.gov/pubmed/24799270 PyDBS: an automated image processing workflow for deep brain stimulation surgery]