Software and Data Processing

MRI and fMRI

Freesurfer: FreeSurfer is a set of tools for the automated analysis of neuroimaging data. This includes the construction of surface models as well as detailed anatomical segmentations and high-resolution inter-subject registration.

GLM Flex: GLM Flex is a set of second-level neuroimaging analysis scripts written as an alternative to the stock SPM8 utilities.

FIVE (Functional Image Visualization Environment): FIVE is a MATLAB-based Orthogonal Slice Viewer designed for looking at fMRI results, with some extra bells and whistles for second-level analyses performed with GLM_Flex.

Image Analysis in Matlab: Toolboxes for diffusion MRI processing, brain connectivity analysis, image registration and segmentation, tissue thickness measurement, etc.

JIP Toolkit: A set of tools optimized for display and analysis of fMRI and PET preclinical data.

NITRC Generalized PPI Toolbox: An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST.

NITRC peak_nii: Statistical image clustering, peak detection and data extraction.

optseq2: optseq2 is a tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events).

Simultaneous MultiSlice (SMS) EPI with Blipped-CAIPI: Pulse sequence and image reconstruction binaries for the Simultaneous MultiSlice (SMS) EPI with Blipped-CAIPI software available for Siemens MRI scanners. Features include: real-time reconstruction of high MultiBand acquisitions, LeakBlock reconstruction for reduced cross-slice signal contamination, and full compatibility between SMS and iPAT for combined slice acceleration and in-plane acceleration.

Highly Accelerated Imaging with Wave-CAIPI: Wave-CAIPI is a parallel imaging technique that allows highly accelerated structural imaging while retaining the image quality. This is achieved by fully utilizing the encoding capability of high-channel count head arrays, allowing an order of magnitude acceleration in 3D and SMS acquisitions. Pulse sequence and image reconstruction binaries for Wave-CAIPI are available for Siemens MRI scanners.  

3D Magnetic Resonance Fingerprinting with Hybrid Sliding-Window and GRAPPA Reconstruction: MR fingerprinting is a novel quantitative imaging approach providing T1 and T2 relaxation maps of the tissue. Our 3D-MRF acquisition/reconstruction dramatically improves SNR efficiency of fingerprinting, thereby providing whole-brain, 1mm isotropic resolution parameter maps in 7.5 minutes.

Optical Imaging

Homer2: Homer2 is a set of matlab scripts used for analyzing fNIRS data to obtain estimates and maps of brain activation.

iso2mesh: iso2mesh is a matlab-based meshing toolbox. It can create 3D tetrahedral finite element (FE) mesh from iso-surfaces and 3D binary volumetric images such as thresholded MRI/CT scans.

Metch: Metch can be used to register the surface mesh created from iso2mesh toolbox.

JSONlab: JSON (JavaScript Object Notation) is a highly portable, human-readable and "fat-free" text format to represent complex and hierarchical data. JSONlab is a free and open-source implementation of a JSON encoder and a decoder in the native MATLAB language.

Monte Carlo eXtreme: Monte Carlo eXtreme (MCX) is Monte-Carlo simulation software for modeling photon migration in 3D turbid media.

Mesh-based Monte Carlo (MMC): Mesh-based Monte Carlo is a Monte Carlo (MC) solver for photon migration in 3D turbid media.

MEG/EEG

MNE: MNE is a software package for processing magnetoencephalography (MEG) and electroencephalography (EEG) data.

PET

JIP Toolkit: A set of tools optimized for display and analysis of fMRI and PET preclinical data.

Pulse Sequence and Image Reconstruction Software

Simultaneous MultiSlice (SMS) EPI with Blipped-CAIPI: Pulse sequence and image reconstruction binaries for the Simultaneous MultiSlice (SMS) EPI with Blipped-CAIPI software available for Siemens MRI scanners. Features include: real-time reconstruction of high MultiBand acquisitions, LeakBlock reconstruction for reduced cross-slice signal contamination, and full compatibility between SMS and iPAT for combined slice acceleration and in-plane acceleration.

Highly Accelerated Imaging with Wave-CAIPI: Wave-CAIPI is a parallel imaging technique that allows highly accelerated structural imaging while retaining the image quality. This is achieved by fully utilizing the encoding capability of high-channel count head arrays, allowing an order of magnitude acceleration in 3D and SMS acquisitions. Pulse sequence and image reconstruction binaries for Wave-CAIPI are available for Siemens MRI scanners.  

General

Neural Spike Train Analysis Tool (nSTAT): The Neural Spike Train Analysis Toolbox for Matlab provides an open-source, object-oriented implementation of methods for neural encoding and decoding analyses. Further information can be found here: Cajigas I, Malik WQ, Brown EN. nSTAT: Open-source neural spike train analysis toolbox for Matlab. J Neurosci Meth. 2012;211(2):245-64. PMCID: PMC3491120.