Software
Below we include software resources developed in our lab, as well as links to software developed by other groups.
Tools are intended to be used to reproduce published study findings and for new analyses.
Choroid Plexus Segmentation
Primary Developer: Kilian Hett
This work uses a fully convolutional neural network, trained on gold-standard radiologist manual tracings, to segment the choroid plexus in the atria of the lateral ventricles from non-contrasted MRI images. This most recent version of the algorithm was developed, and is provided by, Dr. Kilian Hett.
For code, please click here
For explanatory manuscript, please click here
Parasagittal Dural Space Segmentation
Primary Developer: Kilian Hett
This work uses a fully convolutional neural network, trained on gold-standard radiologist manual tracings, to segment the parasagittal dural space in the atria of the lateral ventricles from non-contrasted MRI images. This most recent version of the algorithm was developed, and is provided by, Dr. Kilian Hett.
For code, please click here
For explanatory manuscript, please click here
Asymmetric Spin Echo Analysis
Primary Developer: Alexander Song
This work apply an extravascular signal dephasing model to single or dual echo asymmetric spin echo (ASE) data to quantify oxygen extraction fraction (OEF) and venous cerebral blood volume (CBV).
For code, please click here
For explanatory manuscript, please click here
Horos DICOM Viewer
Primary Developer: The Horos Team (external)
Horos is a free, open source medical image viewer developed by the Horos team. The goal of the Horos Project is to develop a fully functional, 64-bit medical image viewer for Mac OS X. Horos is based upon OsiriX and other open source medical imaging libraries. Horos is made available under the GNU Lesser General Public License, Version 3 (LGPL-3.0).
The Horos software is used for image visualization and was developed externally by the Horos Team.
For software, please click here
For explanatory manuscript, please click here
FMRIB Software Library (FSL) Package
Primary Developer: The FSL Team (external)
FSL is a comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. It runs on macOS (Intel and Apple Silicon), Linux, and Windows (via the Windows Subsystem for Linux), and is very easy to install.
The FSL software is used for image registration, manipulation, and analysis and was developed externally at Oxford University.
For software, please click here
For explanatory manuscript, please click here
Advanced Normalization Tools (ANTs)
Primary Developer: UPenn and Collaborators (external)
ANTs extracts information from complex imaging datasets. ANTs is useful for managing, interpreting and visualizing multidimensional data. ANTs is popularly considered a state-of-the-art medical image registration and segmentation toolkit.
The ANTs software is used for image registration, manipulation, and analysis and was developed externally by researchers at the University of Pennsylvania.
For software, please click here
For explanatory manuscript, please click here