jist:MainPage
From NITRC Wiki
Contents |
Getting Started
The Basics
- Getting MIPAV and Preparing for JIST (Don't worry - it's short.)
- How to Install JIST in MIPAV
- Sight for sore eyes : Font issues
- How to Remove JIST from MIPAV
Advanced Configuration
- How to configure MIPAV and JIST in a Multi-User Environment
- How to build your own JIST directly from NITRC (Again - it's really easy.)
Using JIST Tools
MIPAV Plugin Interface
JIST Visual Scripting Environment
JIST Command Line Environment
Imaging Analysis
Diffusion Tensor Imaging
- JIST-CATNAP (Coregistration, Adjustment, and Tensor-solving – a Nicely Automated Program) is an end to end data processing pipeline. Although [initially developed] in Matlab for Philips PAR/REC Magnetic Resonance data files, this Java-based port for CATNAP supports the data formats supported by MIPAV. CATNAP performs motion correction for both diffusion and structural images using FSL FLIRT, adjusts the diffusion gradient directions for scanner settings (i.e., slice angulation, slice orientation, etc.) and motion correction (i.e., the rotational component of the applied transformation), and computes tensor and derived quantities (FA, MD, colormaps, eigenvalues etc) . The results are readily compatible with DTIStudio, FSL, and other tensor analysis packages.
- JIST-RESTORE (Robust estimation of tensors by outlier rejection) is a popular method of tensor estimation. Here we show how the implementation from CAMINO can be used directly within JIST. http://www.cs.ucl.ac.uk/research/medic/camino/
Robust Estimation of Spatially Variable Noise Fields
- Robust Estimation of Spatially Variable Noise Fields provides a simple mechanism to robustly estimate the voxel-wise noise level through limited repeated acquisitions of multiple contrast modalities. For example, this method would apply if two repetitions of DTI scans were acquired with the same gradient table. There would only be one pair of images for each diffusion weighted direction. However, this method can use the set of image pairs to accurately estimate the complete field.
Quantitative Relaxometry (T1/T2 Mapping)
- T1 Mapping with Double Angle Experiment provides the functionality to estimate T1 tissue properties from 3D-GRE experiments.
- T2 Mapping with Dual Echo Experiment provides the functionality to estimate T2 tissue properties from two echoes of a mutli-slice spin echo experiment.
Multi-Modal CRUISE
- Multi-Modal Cruise is a work in progress. Please stay tuned as we test our wiki-fying skills. --Bennett 05:07, 8 November 2009 (UTC)
Segmentation
- See JIST's use cases for examples of image segmentation.
JIST Development
Developing Plugins
- Tutorial: An Absolute Beginner's Guide to Setting Up JIST
- Save Memory When Writing Plugins
- How to Release a Tool
Integrating Other Platforms
- Documentation in progress.
- Command-line interface
- Network communication (under development)
Getting Help
- Check out our jist:FAQ-QAO - Frequently Asked Questions and Questions Asked Once. (General)
- Check out our jist:FAQ-QAO-DEV - Frequently Asked Questions and Questions Asked Once for JIST Developers. (Development / Programming)
- Please use our trackers to report bugs and/or feature requests: http://www.nitrc.org/tracker/?group_id=228
- Please use our forums for general discussion: http://www.nitrc.org/tracker/?group_id=228
- Our team monitors all of the above lists. However, you are welcome to contact the individual developers directly.
This is only a test...
- This is a test image. If you do not see a tree below, please use the feedback form on the NITRC toolbar and tell the super-cool NITRC folks that the permissions on the wiki-images "broke".
