LONI Resource Research Protocols

Protocols Figure
The LONI Resource provides investigators access to the LONI research protocols. The protocols provide collaborators and researchers with a validated set of methods that will enable them to analyze their brain imaging data. The methods have been implemented to facilitate communications and provide a well defined standard for scientific investigation.

Brain Masking (automatic)	Brain tissue is automatically separated from non-brain tissue
Brain Masking (manual)	Brain tissue is manually separated from non-brain tissue
Cerebellar Sulcal Anatomy	The manual delineation of external and internal primary sulci and fissures of the cerebellum
Cortical Complexity of Cortical Surface	The frequency of sulcal/gyral convolutions in all three planes calculated as the logrithmic least squares regression of surface area against spatial frequency
Cortical Surface Extraction	The extraction of the cortical surface from the skullstripped brain volume
Flat Maps	A flattened/planar map of the cortical surface that retains stereotaxic point locations
Gray Matter, White Matter or CSF Distributions at Cortex	The calculations of concentrations of one tissue type relative to other tissue types, on a point-by-point basis, at the cortical surface
LONI Probabilistic Brain Atlas	Protocols for the construction of the LONI Probabilistic Brain Atlas
Masking Regions of Interest	Protocols for the volumetric parcellation of cortical and sub-cortical regions of interest
Registration	Registration of a subject's brain into a defined standard/average/atlas space.
Segmentation	LONI Segmentation Protocols
Skullstripping	The removal of extra-cortical tissue
Sulcal Anatomy Protocols	The manual delineation of external and internal primary sulci and fissures
Tissue Classification & Segmentation	Brain tissue is classified into gray matter, white matter and CSF and a segmented brain volume is generated based on the tissue classification.