BrainVoyager QX is a powerful neuroimaging software package. It started as a tool for the analysis of anatomical and functional MRI data sets but has evolved over the years into a multi-modal analysis tool for fMRI, DTI, TMS, EEG and MEG data. The software is highly optimized and user friendly running on all major computer platforms including Windows (XP/Vista/7), Linux (i.e. Ubuntu, SUSE, Fedora) and Mac OS X (10.6 or higher).
The Neuroscience Information Framework (NIF) is an initiative by NIH blueprint to bring together all knowledge on neuroscience. Of course DTI is part of this. Find everything NIF put together on DTI here:
Fibernavigator is an interactive diffusion imaging tractography visualization tool. That, as a bonus, is compatible with DTI data processed by FSL. You can download the open-source software for free from their github website (compatible with windows, mac and linux):
When starting out in a new imaging field like diffusion tensor imaging it is easy to be overwhelmed by different processing steps and tools.
A recent publication from Frontiers in Neuroscience tries to offer an answer to most of these questions in their appropriately named article: "A hitchhiker's guide to diffusion tensor imaging". You can find the full manuscript here.
The article discusses sources of artifacts during acquisition and how to reduce/correct them, they go into some detail on how to do quality control (see more on this here), what skull stripping methods are available, how you can use RESTORE for robust tensor estimation, etc.
Most importantly, they supply an exhaustive list of DTI software packages that I adapted into the below table.
Reference: J.M. Soares, P. Marques, V. Alves, N. Sousa (2013). A hitchhiker's guide to diffusion tensor imaging, Frontiers in Neuroscience.
For my own research I use a combination of packages: FSL for preprocessing, Camino for tensor fitting and fiber tracking, DTI-TK for tensor based normalization and TrackVis for visualization and ROI- analysis. ------------------- Reference this post as: Do Tromp, DTI Processing - Software Tools, The Winnower3:e146057.73165 (2016). DOI:10.15200/winn.146057.73165
UCL has recently added a very comprehensive step-by-step guide to tensor fitting with their Camino software.
From their website:
"This tutorial gives an introduction to standard diffusion tensor image fitting with Camino. It gives a step-by-step guide of how to fit the diffusion tensor to data from DTI or HARDI acquisition protocols, how to generate maps of standard markers like mean diffusivity (MD) and fractional anisotropy (FA), and how to generate principal direction and colour FA maps."
"In steps 1-7, we use a human data set and go through the steps to reconstruct and visualize the tensor information, then we do similar reconstruction on some animal data. There is some overlap between the two examples, but in the animal data we look at additional details, and show how to fix the scheme file so that the orientation of the tensors is correct in the image space."
3D Slicer is a great visualization program that has a multitude of tools for analysis of medical images, like registration, segmentation, neurosurgical planning and fiber tracking.
The program provides support for DICOM, NRRD, NIFTI, Tiff, JPG, Freesurfer, FITS and a number of other formats. A comprehensive tutorial on diffusion MRI analysis is provided here.
TrackVis is a software tool that can visualize and analyze fiber track data from diffusion MR imaging (DTI/DSI/HARDI/Q-Ball) tractography. Features of TrackVis include:
Cross-platform. Works on Windows, Mac OS X and Linux with native look and feel.
A variety of track filters (track selecting methods) allowing users to explore and locate specific bundles with ease.
Multiple rendering modes with customizable scalar-driven color codes.
Real-time parameter adjustment and 3D render.
Open format of the track data file allowing users to integrate customized scalar data into the track file and visualize and analyze it. Save and restore scenes in XML style scene file.
Statistical scalar analysis of tracks and ROIs.
Synchronized real-time multiple dataset analysis and display allowing time-point and/or subject comparison. Synchronized analysis and display on same dataset can also be performed in real-time remotely over the network.
Upfront in-line parameter adjustment in real-time. No tedious pop-up dialogs.
You can find a great tutorial and overview on their website: http://trackvis.org/
"Diffusion Tensor Imaging is a cutting edge imaging technique that provides quantitive information with which to visualize and study connectivity and continuity of neural pathways in the central and peripheral nervous system in vivo." -Basser et al, 2000.
Diffusion-imaging.comgives a comprehensive overview of available software, analyzing methods and research possibilities. Providing background on the tools, methods and software to effectively analyze DTI data. Posts include step-by-step processing and tractography tutorials.
Do was born and raised in the Netherlands, where she received her college education in the fields of science & innovation management, psychology and neuroscience. She then continued her education in the United States and received her PhD in neuroscience. During this period she became interested in using diffusion tensor imaging (DTI) to investigate how white matter microstructure may relate to psychopathology. While acquiring the skills to process and analyze this data she noticed the lack of guidelines and support for novice neuroimaging scientists in this field. Therefore, she decided to document all the skills she picked up from working in close collaboration with MRI physicist and DTI experts for nearly a decade and share them online at diffusion-imaging.com. By offering step-by-step tutorials and providing an online community of peers she hoped to provide support for academics worldwide who may not have direct access to DTI experts.
