3rd Party Diffusion MRI Software
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This page is a repository for information about programs that other people have written to process and visualize diffusion MRI data. By examining features of these other programs, we may get inspiration for improvements in our own work.
| Name | Platform | src | inst | Notes |
|---|---|---|---|---|
| Diffusion Processing & Tractography | ||||
| FSL | Lin, Win, Mac | Y | Y | GUI, plus CLI for individual processing steps. Includes implementations of mutual information linear registration, nonlinear registration, brain extraction, qball modelling, stick-and-ball modelling, probabilistic tractography. Includes numerous volumetric atlases. |
| Camino | Java | Y | Y | No GUI. CLI for individual processing steps, connected by Unix pipes. Diverse collection of algorithmic alternatives. |
| Trackvis and Diffusion Toolkit | Lin, Win, Mac | N | Y | Equivalent, respectively, to Brainapp and the diffusion processing pipeline, plus a GUI for the latter. Handles Q-ball imaging as well as DTI. Developed at MGH. |
| MedINRIA | Lin, Win, Mac | N | N | |
| DTI-Query | Lin, Win, Mac | Y | N | |
| CINCH | Lin, Win, Mac | N | N | |
| Freesurfer | Lin, Mac | N | N | GUI, plus CLI for individual processing steps. |
| MRI Studio (formerly DTI Studio) | Win | N | N | Interactive GUI to read/write images, compute DTIs and tractography, and create ROIs. Supposedly also includes Mori, et al.'s 2008 multi-subject DTI-based WM atlas. |
| Brain Voyager | Lin, Win, Mac | N | N | Yet another diffusion MRI GUI program. Commercial license for all users. |
| AMIDE | Lin, Win | Y | N | Graphical tool similar to FSL for viewing, registration, etc. |
| Image Viewing & Conversion | ||||
| AFNI | Lin, Mac | Y | N | A GUI tool for viewing, transforming, and analyzing 2D slice views of images, especially DICOMs. Very powerful, commonly used for published analysis, designed around medical research and clinical uses. |
| OsiriX | Mac | Y | N | A less sophisticated, user-friendlier, AFNI-like GUI tool for DICOM viewing. |
| 3D Slicer | Lin, Win, Mac | Y | N | An even less sophisticated and user-friendlier AFNI-like GUI tool. |
| MRIcron | Lin, Win, Mac | N | N | A GUI viewer for NIfTI. Also includes the dcm2nii DICOM-to-NIfTI conversion program. |
| XMedCon | Lin, Win | Y | Y | Command-line converter for various medical imaging file formats. |
| SPM | Matlab | Y | N | Designed for data sequences, as found in fMRI studies. |
| Diffusion Simulation | ||||
| DifSim | Lin | Y | N | Low-level physics simulations of diffusion MRI response in complex micro-environments. Built on top of MCell. |
See Also
- 3rd Party Visualization Software, which includes toolkits whose functionality is a superset of diffusion MRI processing.
- NITRC, the NIH's Sourceforge-like repository of neuroimaging software
- IDoImaging.com, a database of freeware medical imaging programs and libraries