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Software for Image Analysis

Slicer

Slicer is a mult-platform software package for visualization and medical image computing. Slicer is becoming the standard in resampling, viewing, tracing and performing measurements on medical images. Free for use, one of Slicer’s great advantages is the ability to add custom script to focus on the needs of the researcher.

Brains2

The core software for our structural image analysis. Provides a highly refined user interface for resampling, viewing, tracing, and performing measurements on images. Performs tissue classification, automated structure identification and surface generation. Statistical methods for PET and fMRI analysis are being incorporated. Development is ongoing, and a current collaboration with the ITK consortium complements and improves our software with many new features.

FreeSurfer

A package to generate and manipulate cortical surface representations. We have developed the ability to interface our Brains2 software with FreeSurfer formats to be able to generate spherical or flat maps of the cortical surface. Coregistration of these surfaces to a cortical atlas provides the ability to automate a highly specific parcellation of the cerebral cortex. Surfaces generated with FreeSurfer can also be used in AFNI for the mapping of functional imaging results onto the cortical surface.

AFNI, SPM

Software to process, analyze and display functional images. They have advantages over each other under different situations. The following functionalities are available in both AFNI and the SPM:

Software for Image Analysis

  • 2D and 3D registration (motion correction)

  • Temporal and spatial domain smoothing

  • Linear and non-linear regression of 3D+time series

  • ANOVA tests across a collection of 3D datasets

  • Computation of voxel statistics

  • Computation and color overlay of activation maps

Oracle and PostgreSQL

Relational databases. Implemented with web-enabled query system to provide access to structural imaging measurements, subject demographics and results from clinical assessments and cognitive and neuropsychological testing.

GoToMeeting/Lync

INC has purchased an account with GoToMeeting, a web conferencing and online meeting program. This enables us to have a meeting with anyone in the world. Meetings can be in large or small groups, or even in a single office. We also have access to Lync which allows video collaboration with people in and outside the University of Iowa.

XCode

Xcode is an integrated development environment containing a suite of software development tools developed by Apple for developing software for OS X and iOS systems. Xcode takes advantage of all the newest Apple technologies by integrating all the tools needed to create source code, debug programs, and design user interfaces.

MATLAB

Matlab is a high-level language and interactive environment for numerical computation, visualization, and programming. MATLAB allows users to analyze data, develop algorithms, and create models and applications.

Osirix/DicomRemap

OsiriX is an image processing application for Mac dedicated to DICOM images. OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D, 3D, 4D and 5D viewers.

Jira

A web interface and bug-tracking package to allow users to create and modify bug reports in a simple database. This provides excellent feedback to our developers from users at any site.

Confluence

Web based wiki program that is used for project and information sharing and tracking.

PET analysis

A set of programs that provides capability for many types of analysis of PET data, including within-group analysis via techniques by Worsley et al. (the Montreal method), voxelwise correlational analysis and randomization analysis. Includes a sophisticated image viewer for easy review of results.

Research