Segmentation tools for the quantification of peri-sinus space using non-invasive MRI developed by Dr. Kilian Hett.
Choroid plexus segmentation
A segmentation tool for the delineation and volumetric quantification of the choroid plexus developed by Dr. Kilian Hett.
Arterial Spin Labeling
Matlab-based arterial spin labeling (ASL) software developed by Dr. Manus Donahue (Vanderbilt University Medical Center). The ASL software toolkit is designed to process Philips PAR/REC and DICOM ASL images and includes functionality for motion correction, labeling efficiency correction, T1-correction for hematocrit, slice time correction, surround subtraction, and utilizes the simplified ISMRM Perfusion Study Group kinetic model for cerebral blood flow (CBF) determination. Motion correction requires FSL installation.
Vandpire ASL Toolbox
Vandpire ASL Toolbox: A Novel Data-processing Pipeline for Imaging Research (VANDPIRE) developed by Dr. Daniel Arteaga and Manus Donahue (Vanderbilt University Medical Center). VANDPIRE is an intuitive and comprehensive software for quantifying cerebral blood flow (CBF) and calculating CBF territories based upon arterial spin labeling (ASL) MRI data. CBF analysis, particularly CBF territory analysis, is time-consuming and requires an advanced knowledge of scripting and up-to-date mathematical models. As a result, many researchers who are interested in performing such analyses are unable to do so. This toolbox addresses these concerns, and additionally is available on multiple platforms as a graphical user interface, making such analyses much more accessible to researchers. Academic users may license and download the VANDPIRE software free of charge.
Rapidtide
Rapidtide; developed by collaborator Dr. Blaise Frederick (McLean Hospital and Harvard University). The rapidtide suite is a set of python tools that we've developed and tested over the last several years in the McLean Hospital Opto Magnetic Group to perform rapid time delay analysis on functional imaging data to find time lagged correlations between the voxelwise time series and other time series. This technique can be used to detect, quantify, and display blood-borne physiological noise signals, as a method for quantifying hemodynamic parameters, and/or as a way to remove them from datasets to improve fMRI data quality.
FMRIB Software Library
FMRIB Software Library (FSL) developed by members of the Oxford Centre for Magnetic Resonance Imaging of the Brain.
Flow Territory Map Atlas
flow territoriesFlow territory map atlas developed by Dr. Manus Donahue. A flow territory probability atlas of left and right internal carotid artery (ICA) and vertebrobasilar artery flow territories calculated from 158 subjects using vessel-encoded pseudocontinuous arterial spin labeling (VE-pCASL). The atlas is in 2 mm Montreal Neurological Institute Space.