Primatologist Toolbox: Pipeline blocks

This category contains individual blocks used in the Primatologist pipeline. They are intended to be used in combination with databases.

Content

Preprocessing and Atlas Registration

• Prepare MRI: orient the MRI volume based on landmarks.
• Align and Resample: rigid alignment using landmarks and resampling at a fixed resolution.
• VIP Bias Correction: VIP bias correction.
• Skull-Strip MRI: compute a skull-stripping mask.
• Atlas Registration: Select Evaluation Points: random selection of evaluation points in the reference image space.
• Atlas Registration: Affine (MI/Newton): affine registration by optimization of mutual information.
• Atlas Registration: Non Linear (MI/FFD): non linear (FFD) registration by optimization of mutual information.
• Atlas Registration: Application: application of the affine+FFD transformation to the atlas.

Bayesian segmentation

• Basic Mixture Fitting: initialize GMM parameters with a naive mixture + prior map preprocessing.
• Brain Parcellation (EM): MRI bayesian segmentation with noise and bias estimation.

Prepare for Morphologist

• Compute and Split Brain Mask: compute a Morphologist-compatible split brain mask.
• Grey White Classification: compute a Morphologist-compatible gray-white mask.
• Histogram Analysis (for Morphologist): compute a Morphologist-compatible histogram analysis.
• Invert: invert T2-weighted images to make them lok like T1-weighted images.
• Talairach Transformation: compute a transform to Talairach space.

Surfaces and Sulci Extraction

• Cortex Topological Correction: compute the topologically correct white mask.
• White Matter Mesh: compute the white matter mesh with Morphologist.
• Sulci Skeleton: compute the sulci skeleton with Morphologist.
• Pial Mesh: compute the pial mesh with Morphologist.
• Cortical Folds Graph: compute cortical folds with Morphologist.
• Sulci Voronoi: compute sulcal catchment bassins with Morphologist.
• Sulci Thickness and Volumes: compute sulcal statistics with Morphologist.