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.

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¶

Atlas view in 3D: see this little demo

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

_images/anat_landmark_picture-2_small.jpg — Probability maps¶

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

_images/atlas_sulci_small.jpg — Outlines¶

The outline at 50% of all the structures

_images/nomenclature_small.jpg — 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).

_images/poster_hbm11_perrot_m_small.jpg — HBM 2011 poster¶

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

_images/nomenclature_translation_small.png — Atlas of Sulci with nomenclature table (2018)¶

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