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MRI Analysis Tools
Here is a list of various MRI software tools and helps to get you started analyzing data. This is not an exhaustive list but covers some popular freely available tools. Some of the tools below are more user-friendly than others but the tools below have great support from developers and users.
What kind of computer do you need to analyze MRI? Macs are great for most MRI analysis work. Linux can be more powerful but is more difficult to support. Depending on the particular analysis, however, Linux might be the best option. Windows is great for any Matlab-based tools (e.g., SPM) but many of the tools below are Linux and/or macOS native. The Windows 10 Anniversary Update added a way to use Linux bash (command line) tools; it works well for many tools but has limitations with others.
If you have at least a basic working knowledge of the command line (bash shell or similar), you will be more successful using the software listed below. There are many guides online to get you started.
If you need neuro software/tools or neuroimaging data, NITRC is a great resource. It’s one of the best places to start to see what tools are available.
NeuroDebian is a Linux repository that provides a large collection of popular neuroscience research software for the Debian operating system as well as Ubuntu and other derivatives. Popular packages include AFNI, FSL, PyMVPA and many others.
- FreeSurfer: http://freesurfer.net
- FSL
- ITK-SNAP
- Advanced Normalization Tools (ANTs) provides many sophisticated tools for analyzing brain structure
- FreeSurfer TRACULA
- FSL has various diffusion tools
- TrackVis and Diffusion Toolkit
- MRtrix
- ExploreDTI
- Camino