Morphologist¶
Brain segmentation and sulcal analysis
- 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. link bibtex-entry
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¶
Morpho-DeepSulci¶
SulPatEd¶
Sulpated, “Sulcal Patterns Editor” is a graphical interface to manually label sulci and sulcal patterns. See the doc in the dedicated page.
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.
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 link bibtex-entry paper
- PERROT2011
Perrot, D. Rivière, and J.-F. Mangin. Cortical sulci recognition and spatial normalization. Medical Image Analysis 2011 link bibtex-entry 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 link bibtex-entry 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 link bibtex-entry 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 paper