Software

Software designed at the IDeA Lab consists of Linux-based tools for all phases of visualization and image analysis, and is freely available to the public.

This page also includes a package of brain template images and ROIs used in our lab.

We frequently update the packages. You are welcome to check back for recent updates and bug fixes. If you have any questions, please contact Evan Fletcher directly by email.

File Manipulation Utilities
A set of utilities for manipulating images and managing file formats.

Stroke Viewer
A user interactive tool for viewing and rating strokes.

Image Segmentation (Tissue Classification)
Mri tissue classification program.

UCD WMH Segmentation
Pipeline for automatic identification of white matter hyperintensities in native space.

WMH Detection
Automatic identification of white matter hyperintensities in template space.

Multiple Atlas Brain Extraction (ICC)
T1 image fully automatic skull removal using multiple atlases.

Multiple Atlas Hippocampus And Ventricle Extraction (HCV)
Fully automatic Multi-Atlas segmentation of hippocampus as per the Harmonized Hippocampal Protocol and ventricles for T1 images.

Visualization
Slice-based viewing and cleanup tools.

Preprocessing
Automated skullstrip and alignment of slices if necessary.

MRI Bias Correction
Template-based MRI inhomogeneity correction for stripped brain images.

Image Alignment
Used for longitudinal or cross-sectional studies. This involves linear alignment of pairs of images and high-dimensional warping of a template image onto subject images.

Brain Tissue Loss Measurement
We have implemented the Brain Boundary Shift Integral algorithm.

GUI Image Analysis Tool
A user interactive tool for image processing. It implements a pipeline of steps that involve TCV tracing, slice-based TCV image bias removal, brain vs non-brain segmentation, filtering of DSE images, modeling of white matter hyperintensities and tracing of ROIs. Generates numerical reports in csv format.

Download a powerpoint tutorial for the Image Analysis Pipeline here.

Subject Library
A tool for searching through a collection of MRI scans and reporting on the pipeline status of each scan session. This is a filesystem-based utility, that can be configured to fit many different organization schemes. This package also contains the 'idealab.tools' python library. This can be used to write scripts that iterate through and manipulate studies, subjects, scan sessions, etc.

Idealab Neuroimaging Data Management Tools
Includes 'subjectlibrary' and 'qtdimp'. 'subjectlibrary' is a tool for searching through a collection of MRI scans and reporting on the pipeline status of each scan session. This is a filesystem-based utility, that can be configured to fit many different organization schemes. 'qtdimp' is a dicom importer. It can be used to assemble dicoms into 3D volumes and to import them into an organized filesystem.

Brain Template and ROI Images
We offer a "Minimal Deformation Template" (MDT3) brain image and an array of corresponding ROI (region of interest) masks. MDT3 represents an average normal elderly subject designed to match a range of normal elderly subjects with minimum deformation after linear alignment. The ROIs drawn on MDT3 represent commonly used regions including all the lobes, corpus callosum, and Brodmann areas.

List of Template and ROI files

All of these images are available in a tar.gz file which can be downloaded using the download link below. After clicking this link and the copyright consent, please click on the box for "IDeA Lab Brain Templates and ROIs".

Index of Downloadable Applications

1. Click on the link below or here to access the copyright page.
2. Click "Agree and continue" to proceed to the selection form.
3. Click the boxes that apply to the packages desired, then the "Submit" button. This will give you one or more links to tar.gz packages for download.
4. To unpack the tar.gz package on your computer, copy it to the desired location (typically /usr/local/bin) and execute:

   tar xvzf packagename.tar.gz

   where "packagename" is the individual name of the downloaded package.

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