Brain segmentation and sulcal analysis

  1. Fischer, G. Operto, S. Laguitton, M. Perrot, I. Denghien, D. Rivière, and J.-F. Mangin: Morphologist 2012: the new morphological pipeline of BrainVISA, In Proc. HBM, 2012.

A more complete doc is available here

Morphologist UI

Morphologist now has a new graphical interface, featuring simplified user experience and quick interactive visualization:


Docmentation can be found here

It can be run either as a standalone program (morphologist), or through BrainVISA.

Morphologist toolbox in Brainvisa

BSA Atlas (Brainvisa Sulci atlas) v.2011

This atlas gives the probability of finding various cortical folds or gray nuclei across a population.


Probability maps

Probability maps corresponding to a few anatomical landmarks (cortical folds) overlaid on a T1 template



The outline at 50% of all the structures


Labels location

Location of sulcal labels mapped on a 3D representation of a refined version of the anatomical atlas (after a sulcuswise non-linear registration scheme).


HBM 2011 poster

A high-resolution full-brain probabilistic atlas of regions based on cortical folds


Atlas of Sulci with nomenclature table (2018)

Location of sulci named by their Brainvisa acronyms or their full anatomical names



Atlas estimation

  1. Perrot, D. Riviere, A. Tucholka, J.-F. Mangin : Joint Bayesian Cortical Sulci Recognition and Spatial Normalization, IPMI 2009 paper

  1. Perrot, D. Rivière, and J.-F. Mangin. Cortical sulci recognition and spatial normalization. Medical Image Analysis 2011 paper


Defining anatomo-functional parcels

Alan Tucholka, Bertrand Thirion, Matthieu Perrot, Philippe Pinel, Jean-François Mangin and Jean-Baptiste Poline : Probabilistic Anatomo-Functional Parcellation of the Cortex : How Many Regions ?, MICCAI 2008 paper

Refining functional MRI analysis

Merlin Keller, Marc Lavielle, Matthieu Perrot and Alexis Roche. Anatomically Informed Bayesian Model Selection for fMRI Group Data Analysis. MICCAI 2009 paper

Functional connectivity

Gaël Varoquaux, Alexandre Gramfort, Jean-Baptiste Poline, Bertrand Thirion. Brain covariance selection : better individual functional connectivity models using population prior. NIPS 2010 link