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.
We frequently update the packages. Updates are listed in the UpdateLog and the date of the current version is displayed in the README file of each download directory. You are welcome to check back for recent updates and bug fixes. If you have any questions, please contact Evan Fletcher directly by email.
Descriptions of Packages
A set of utilities for manipulating images and managing file formats.
Slice-based
viewing and cleanup tools.
Automated skullstrip and alignment of slices if necessary.
Template-based MRI inhomogeneity correction for stripped brain images.
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.
We have implemented the Brain Boundary Shift Integral algorithm and we
also use a fluid-flow jacobian algorithm for detecting tissue loss in longitudinal images
(this will be posted soon).
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.
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.
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