Morphologist

Brain segmentation and sulcal analysis

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[FISCHER2012]

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.

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

• Slides on the Morphologist pipeline
• Morphologist toolbox documentation
• Developers documentation

BSA Atlas (Brainvisa Sulci atlas) v.2011

• Atlas view in 3D: see this little demo

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

Outlines

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

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

Downloads

• Download the Atlas (nii.gz file, 71Mo, in MNI space, 2mm isotropic voxels)
• Table giving the names of the anatomical structures (csv file)
• CSV of anatomical structures - fields : index, location (x,y,z), color(r,g,b), brainvisa acronym and anatomical label.
• Table of sulcal labels - Meanings of Brainvisa acronyms used for sulcal structures
• The older sulci labels used before BrainVisa/Morphologist 3.2, and handled by the older ANN models 2001. There are slight changes, but there are changes.

References

Atlas estimation

[PERROT2009]

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

[PERROT2011]

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

Applications

Defining anatomo-functional parcels

[TUCHOLKA2008]

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

[KELLER2009]

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

Functional connectivity

[VAROQUAUX2010]

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