Morphologist ============ Brain segmentation and sulcal analysis .. .. raw:: html .. :file: carousels/car_morphologist_big.html .. [FISCHER2012] C. 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. :web:`link ` :web:`bibtex-entry ` Morphologist UI --------------- Morphologist now has a new graphical interface, featuring simplified user experience and quick interactive visualization: .. image:: _static/images/morphologist-ui.jpg :width: 50% :target: ../morphologist-ui/index.html Docmentation :morphouiusr:`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:`Morphologist pipeline ` * :morphoproc:`Morphologist toolbox documentation ` * :morpho_api:`Developers documentation ` Morpho-DeepSulci ---------------- * :morphodeep_dev:`The new (2019) sulcal identification algorithms and processes ` SulPatEd -------- Sulpated, "Sulcal Patterns Editor" is a graphical interface to manually label sulci and sulcal patterns. See the doc in the dedicated page. :doc:`sulpated` BSA Atlas (Brainvisa Sulci atlas) v.2011 ---------------------------------------- * Atlas view in 3D: :morphologist:`see this little demo ` This atlas gives the probability of finding various cortical folds or gray nuclei across a population. .. figure:: _static/images/bsa/anat_landmark_picture-2_small.jpg :target: _static/images/bsa/anat_landmark_picture-2.png :width: 50% Probability maps Probability maps corresponding to a few anatomical landmarks (cortical folds) overlaid on a T1 template .. figure:: _static/images/bsa/atlas_sulci_small.jpg :target: _static/images/bsa/atlas_sulci.png :width: 50% Outlines The outline at 50% of all the structures .. figure:: _static/images/bsa/nomenclature_small.jpg :target: _static/images/bsa/nomenclature.png :width: 50% 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). .. figure:: _static/images/bsa/poster_hbm11_perrot_m_small.jpg :target: _static/images/bsa/poster_hbm11_perrot_m_150dpi.jpg :width: 50% HBM 2011 poster A high-resolution full-brain probabilistic atlas of regions based on cortical folds .. figure:: _static/images/bsa/nomenclature_translation_small.png :target: _static/images/bsa/nomenclature_translation.png :width: 50% 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 <_static/images/bsa/anat_landmark_atlas.csv>`_ (csv file) * `CSV of anatomical structures <_static/images/bsa/anat_landmark_atlas.csv>`_ - fields : index, location (x,y,z), color(r,g,b), brainvisa acronym and anatomical label. * `Table of sulcal labels <_static/images/bsa/anat_landmark_atlas_table.pdf>`_ - Meanings of Brainvisa acronyms used for sulcal structures * The :documents:`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] M. Perrot, D. Riviere, A. Tucholka, J.-F. Mangin : **Joint Bayesian Cortical Sulci Recognition and Spatial Normalization**, *IPMI* 2009 :web:`link ` :web:`bibtex-entry ` `paper `_ .. [PERROT2011] M. Perrot, D. Rivière, and J.-F. Mangin. **Cortical sulci recognition and spatial normalization**. *Medical Image Analysis* 2011 :web:`link ` :web:`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 :web:`link ` :web:`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 :web:`link ` :web:`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 `_