Project Week 25/Surgical Planning In Stereotaxy - Revision history

Fepegar at 13:00, 30 June 2017

2017-06-30T13:00:53Z

Fepegar: Edit colormap image

2017-06-30T12:57:51Z

Edit colormap image

Fepegar: Make images larger

2017-06-30T12:38:38Z

Make images larger

Fepegar at 12:36, 30 June 2017

2017-06-30T12:36:24Z

Fepegar: Fill progress and next steps section

2017-06-30T10:15:15Z

Fill progress and next steps section

Marianna at 15:37, 26 June 2017

2017-06-26T15:37:36Z

Fepegar: Edit affiliations

2017-06-26T09:07:08Z

Edit affiliations

Fepegar: Add Slicer developers' affiliations

2017-06-24T15:47:47Z

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Fepegar: Add project page

2017-06-24T15:43:28Z

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__NOTOC__

Back to [[Project_Week_25#Projects|Projects List]]

==Key Investigators==

* Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
* Csaba Pinter
* Andras Lasso
* Steve Pieper

==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;"
|
* Improve the graphical user interface of the modules
* Generalize the modules for different stereotaxy procedures
* Adapt the modules logic to use the new Segmentations

|
* 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

|

|}

==Illustrations==

[[File:Pydbs module.png|thumb|Post-operative scene in Deep Brain Stimulation (DBS)]]

==Background and References==

* [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]

@@ Line 38: / Line 38: @@
 ** Get inspiration from commercial consoles
 ** Ask neurosurgeons for feedback
-* A [https://github.com/Slicer/Slicer/pull/741 pull request] for a new colormap has been created
+* A [https://github.com/Slicer/Slicer/pull/741 new diverging colormap] has been contributed
 |}
 ==Illustrations==

@@ Line 45: / Line 45: @@
 [[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: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==

@@ Line 43: / Line 43: @@
 ==Illustrations==
 [[File:Pydbs module.png|600px|thumb|left|Post-operative scene in Deep Brain Stimulation (DBS)]]
-[[File:YeB atlas segmentation.jpg|600px|thumb|left|Segmentation representing a histological atlas of the basal ganglia and segments tables included in the GUI]]
+[[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|600px|thumb|left|Visualization of FreeSurfer segmentation for the assessment of stereotactic surgery in epilepsy]]
+[[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|600px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear deformation]]
+[[File:Diverging colormap for Jacobian visualization.png|800px|thumb|left|Different colormaps used to visualize compression and expansion after a non-linear deformation]]

@@ Line 8: / Line 8: @@
 * Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
 * Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
-* Csaba Pinter (Queen's University, Canada)
+* [http://perk.cs.queensu.ca/users/pinter Csaba Pinter] (Queen's University, Canada)
-* Andras Lasso (Queen's University, Canada)
+* [http://perk.cs.queensu.ca/users/lasso Andras Lasso] (Queen's University, Canada)
-* Steve Pieper (Isomics, Inc., USA)
+* [http://www.spl.harvard.edu/pages/People/pieper Steve Pieper ] (Isomics Inc., USA)

@@ Line 8: / Line 8: @@
 * Sara Fernández-Vidal ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
 * Fernando Pérez-García ([http://icm-institute.org/en/ Brain & Spine Institute], Paris, France)
-* Csaba Pinter (Queen's University)
+* Csaba Pinter (Queen's University, Canada)
-* Andras Lasso (Queen's University)
+* Andras Lasso (Queen's University, Canada)
-* Steve Pieper (Isomics, Inc.)
+* Steve Pieper (Isomics, Inc., USA)

@@ Line 34: / Line 34: @@
 |<!-- Progress and Next steps (fill out at the end of project week), bullet points -->
+* Segmentations have been integrated in the core of the toolbox
 |}
 ==Illustrations==
 ==Background and References==