NA-MIC Project Weeks

New 3D Slicer extension for the YEB Atlas.

Key Investigators

Sara Fernandez Vidal (ICM, Paris Brain Institut. Stereotaxy Platform, https://institutducerveau-icm.org/en/cenir-stim/)
Eric Bardinet (ICM, Paris Brain Institut. CENIR Platform. )
Severine Chandelier (ICM, Paris Brain Institut. Scientific Computing. IT Departement.)

Project Description

The YEB Atlas is a Basal Ganglia atlas used in routine clinical practice at the Pitié Salpêtrière Hospital in DBS-related procedures, both preoperatively (planning/targeting) and postoperatively.
It is also widely used in multicenter research studies. We cannot share the atlas as a fully open free atlas because it is bound to Medtronic by a strict license agreement. That’s why in 2021, we set up a web service for the YEB atlas that allows to get deformed atlas regions on the uploaded anatomical MRI in NIFTI format. WEB PAGE.

Currently we are setting up a REST API on the same server. The main idea is that this new extension will connect with the API to get a set of regions (we will give some choices) of the atlas in a anatomical brain MRI. One of the advantages using 3D Slicer is that the user will be using other formats than nifti that is actually the only allowed on the web server platform. A second advantage is to use the segmentation module of 3D Slicer. Another utility should be to launch the process for a group of subjects. This extension will also be used in a new module dedicated to assist the DBS targeting stage.

Objective

The first objective is to create an initial prototype of the Extension with a curl request to de API and the import of the YEB segmentation to the Slicer Scene

Approach and Plan

To exchange with the 3D Slicer community about differents points lookup tables/ontologies and segmentations, requests, …

Progress and Next Steps

For this firt prototype Module, I launch Atlas Yeb Registration from Docker Image (and not from API) and create the segmentations objects from the results of the process.
Nexts steps will be to give the choice to launch the AtlasYEB Registration From the WEB API or from the docker. Explore the use of terminologies and modify the GUI of the module to choose the regions to save as mask or labelmaps. Verifiy the description of the structures … And publish the Extension

Illustrations

[AtlasYEB Registration Result]

[Inmporting Models to Segmentation Objects]