Software

cortical_surfaceWe are developping the Cortical Surface toolbox that comes included in the official BrainVisa distribution.

Below you can find some information and documentation about some pipelines of the Cortical Surface toolbox. Documentation and tutorials will be added over time in order to show how to use pipelines and what to do with them.

Most of our pipelines need the Morphologist Pipeline to be run beforehand, in order to have triangular meshes of the cortical surface and all sulci, as well as a labelling of these sulci.

People who have contributed to the toolbox are: Guillaume Auzias, Olivier Coulon, Grégory Operto, Arnaud LeTroter, Denis Rivière, and Cédric Clouchoux.

Pipelines:

Ressources:

Hip Hop

Cortical surface parameterization and inter-subject matching This process performs a parametrization of the white matter surface, and implicitely provides an inter-subject cortical surface matching. The resulting 2D coordinate system (longitude/latitude) is fitted to a model of cortical organization, which means that a number of sulcal lines have a constant coordinate (longitude or latitude) and that …

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HipHop138

Cortical Surface group template DOWNLOAD In order to have a reference surface for group studies, we built a surface template of the cortical surface. The HipHop138 template has been built by averaging the surfaces of 138 subjects after running the HipHop surface parameterization on these subjects. Both hemispheres have been processed separately.   HipHop138 is …

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MarsAtlas

Cortical parcellation model MarsAtlas is a model of cortical parcellation. It can be applied to any cortical surface via the HipHop parameterization pipeline, available in the BrainVisa Cortical Surface Toolbox, under the Anatomy category. MarsAtlas has been developed in collaboration with Andréa Brovelli at INT. It has been primarily designed for functional data analysis and …

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MarsAtlas + subcortical

Adding subcortical structures to the MarsAtlas cortical parcellation MarsAtlas is a model of cortical parcellation. It can be applied to any cortical surface via the HipHop parameterization pipeline, available in the BrainVisa Cortical Surface Toolbox, under the Anatomy category. MarsAtlas has been developed in collaboration with Andrea Brovelli and Guillaume Auzias at INT. You can …

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Sulcal parameterization

This process performs a length-parameterization of  sulcus meshes. This is useful to study the morphology of sulci and localize features on them. The sulcus needs to have been identified and labelled automatically or by hand before, and is modeled by a triangular mesh. The result is a coordinate field that localize any point on the …

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