Project: Integration of Jülich Brain Atlas to 3D Slicer EpiSTIM project

[sarafv]

Draft Status

Draft - team will hold off on page creation

Category

Segmentation / Classification / Landmarking

Key Investigators

• Sara Fernandez Vidal (Paris Brain Institute, France)
• Valerio Frazzini (Paris Brain Institute - APHP, France)

Project Description

We intend to integrate the Julich Brain Atlas into our EpiSTIM 3D Slicer Extension.

EpiSTIM is a software project developed to assist neurosurgeons, neurologists and researchers in image processing tasks related to SEEG surgical procedures, from surgical stereotaxic planning to postoperative studies.

The Julich-Brain Atlas (Amunts et al. Science 2020) contains cytoarchitectonic maps of more than 200 areas of the human brain including cortical areas and subcortical nuclei. This atlas is widely used in the epileptology community both in SEEG planning and postoperatively to localize intracranial activity recorded during clinical cognitive tasks or other types of tasks.

The Julich-Brain is the foundation of the Multilevel Human Brain Atlas, which integrates neuroanatomical features with complementary maps of the molecular architecture, function and connectivity across multiple scales and is openly available to the research community via the Human Brain Project’s research infrastructure EBRAINS.

Objective

1. Objective A. Describe what you plan to achieve in 1-2 sentences.

Approach and Plan

1. Download the two versions of Julich Brain Atlas (on fsaverage and MNI templates) and visualize in 3D Slicer atlas.
2. Add Julich atlas terminology to the slicer
3. Add Julich data and terminology in EpiSTIM resources.
4. Map the Julich on Subject natif space for the planning module of the SEEG procedure
5. Add the Julich maps on the MNI visualisation of the postoperative reconstruction of the SEEG procedure

Progress and Next Steps

1. Describe specific steps you have actually done.

I spent the most time exploring the latest Julich dataset published on EBRAIN and adapting the formats of certain annotations, colormaps and ontologies (thanks to Mura) to 3D Slicer. In the first figure you can see one of the labelsmap in the MNI template.
And in the second one the Julich anotations in the Freesurfer Fsaverage template in the pial and inflate surfaces.

I think I will prepare a 3D Slicer module to easily visualize and navigate all components, especially probability maps.

Illustrations

Postoperative SEEG reconstruction EpiSTIM module

Jülich Brain Atlas

Jülich Brain Atlas in 3D Slicer

Background and References

Jülich Atlas 👍 https://www.fz-juelich.de/de/inm/inm-1/aktuelles/meldungen/complete-data-package-of-julich-brain-atlas-released

No response

[sarafv]

?

[sjh26]

?

?

Is this ready to be moved from draft status?

[sarafv]

Hi, non! It was a try … See you on Monday Sara

…

Le 21 janv. 2025 à 16:23, Sam Horvath ***@***.***> a écrit : ? ? Is this ready to be moved from draft status? — Reply to this email directly, view it on GitHub <#1372 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGMGNPPPH7NZZCX45AU4EWL2LZQ6PAVCNFSM6AAAAABVSKRSWKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMBVGAZTANJTGE>. You are receiving this because you authored the thread.

[github-actions]

Project Page Pull Request Creation

✅ COMPLETED: See #1402