Software Resources

PET & MRI Image & Data Processing Resources

Image processing services, software tools, and high-speed computing servers are available through the MR and PET Research Centers.

“Off-the-shelf” tools may include the following software packages that may be acquired from the University Computing Services and Systems Development (CSSD) or downloaded from the web.

Brain Processing Tools

AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.

BioImage Suite is a broad range of structural and functional image processing tools that also covers cardiac and abdominal imaging and animals.

BrainSuite is a MRI analysis tool for visualizing, identifying, segmenting, and labeling brain tissue types and surfaces, and extracting cortical surfaces.

BrainVoyager is a suite of software for analysis and visualization of structural and functional MRI and MEG/EEG data.

DPTOOLS is a suite of brain image processing tools including fMRI, perfusion and diffusion MRI.

Freesurfer allows visualization of the functional regions of the highly-folded cerebral cortex. It contains both volume based and surface based analysis, which primarily use the white matter surface.

FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.

Functional MRI Analysis and Clustering Tools (FACT) is a suite of fMRI processing tools.

Medical Imaging ToolKit (MITK) is an open-source c++ library for medical image processing.

MIPAV (Medical Image Processing, Analysis, and Visualization) application enables quantitative analysis and visualization of medical images of numerous modalities such as PET, MRI, CT, or microscopy.

MRIConvert and Mcverter convert DICOM images to other formats.

Neurostat/3D-SSP is a software library for processing neurological and biomedical image including multiple modalities.

Physiological Artifact Removal Tool (PART) is used to remove physiological noise from fMRI data.

PMOD consists of a set of user-friendly and powerful tools, each corresponding to a major task. The general modeling tool contains a comprehensive set of models for the analysis of time-activity data. With the pixel-wise modeling tool specialized models can be applied to calculate functional maps showing absolute tissue parameters. The cardiac modeling tool is tailored to assess function in cardiac segments by full kinetic modeling, and to compare the outcome against normal databases. The image fusion tool not only allows to register images, but also enables the user to explore the calculated functional images in detail. Further interactive investigation is facilitated by the versatile 3D rendering tool. A fully automatic analysis of FDG data from patients with suspected Alzheimer's dementia is provided by the Alzheimer's discrimination analysis tool which is based on the outcome of a vast multi-center trial. Based on the normal brain database tool users can implement unique strategies to establish their own brain analysis procedure for new tracers or specific diseases.

Resting-State fMRI Data Analysis Toolkit is a Matlab base suite of programs for brain analysis.

QuickVol II is a simple too for processing MRI and fMRI data that runs in ImageJ.

Signal Processing in NMR (SPIN) is a Visual C++, Windows-based software for processing perfusion, angiography, and diffusion MRI.

SPM is designed for the analysis of fMRI, PET, SPECT, EEG and MEG brain imaging data. The sequences can be a series of images from different cohorts, or time-series from the same subject. SPM is run on a platform of Matlab.

TrackVis and Diffusion Toolkit are software tools that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography.

Perfusion Data Analysis

COMKAT is compartmental modeling software for biomedical applications.

Perfusion Mismatch Analyzer (PMA) is used for processing quantitative analysis of perfusion and diffusion imaging associated with stroke.

DCE

DATforDCEMRI performs voxel-wise deconvolution analysis of DCE-MRI and runs in the R environment.

DCEMRI is open-source code for processing Dynamic Contrast Enhanced (DCE) and Diffusion Weighted Imaging (DWI) MRI data intended for oncology applications. DCEMRI runs in the R programming environment.

Toppcat is used to process T1-weighted Dynamic Contrast Enhanced (DCE) MRI.

DSC

DSCoMAN is used to process T2* weighted dynamic susceptibility contrast (DSC) MRI.

ASL

Arterial Spin Labeling (ASL) MRI Processing Software (MGH) covers various forms of ASL.

ASL Data Processing Toolbox is used to calculate cerebral blood flow and runs in Matlab.

Diffusion Tensor Data Analysis

Brain Connectivity Toolbox is a Matlab suite of programs for characterizing brain connectivity.

ExploreDTI is a graphical toolbox for DTI and fiber tractography.

DSI Studio can be used for analyzing DTI, Diffusion spectrum imaging (DSI), Q-Ball, and generalized Q-sampling imaging.

medInria is visualization software that can be used for tractography.

MRI Studio is a Windows-based program for DTI analysis.

UCL Camino Diffusion MRI Toolbox is an open-source toolbox that covers standard and custom DTI analyses.

Relaximetry

MRI Processor, MRI Analysis Calculator, MRI T2 Calculations generate T1 and T2 parametric maps and runs in ImageJ.

Animal Image Processing Tools

3D Pulse-coupled Neural Networks (PCNN) for rodent brain extraction.

JIP fMRI Analysis Toolkit is open-source c-code for the analysis of structural and functional rodent and non-human primate fMRI data.

General Image Viewers

3D Slicer is open source software for visualization of medical imaging data and has many built-in features.

AMIDE is a viewing, analyzing, and registration toolkit.

ImageJ is an image processing and analysis program that supports multiple image formats (GIF, JPEG, ASCII, BMP, DICOM, and FITS).

K-PACS is a DICOM image viewer.

MRIcro can view various medical image formats, including the Analyze format used by SPM. Analyze format images have two components: the image file (.img) that contains the raw image data and a header file (.hdr) that describes the image dimensions, data format and comments. MRIcro's header information panel displays the header file's information and includes a series of buttons that allow you to open and view headers.

Osirix is an image processing application dedicated to DICOM images that is designed for Apple platforms (Mac, iPhone, iPad).

VolView is an open-source volume visualization tool.

Statistical Processing Software

R is a software environment for statistical computing and graphics.

SPSS Statistics is a comprehensive, easy-to-use set of predictive analytic tools for business users, analysts and statistical programmers.

Cardiac Imaging

Segment is a cardiac image processing and analysis program for multiple modalities including MRI, CT, and SPECT.

Programming Software Platforms

IDL is a numerical computing environment that is used for image and data processing and display.

MatLab is a numerical computing environment and fourth-generation programming language. Developed by MathWorks, MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, and Fortran.

Microsoft Visual Studio C/C++ is used for pulse sequence programming and data/image reconstruction on the Siemens MRI and PET/MRI (mMR) systems using the Siemens IDEA/ICE compilers.

Wolfram Mathematica is a high-level programming and simulation environment that supports analytic and numerical solutions and provides graphical displays.

Image Templates

Brain Atlases

Montreal Neurological Institute (MNI)

University of Pittsburgh Elderly Cohorts

Functional ROIs has over 90 brain ROIs