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| # neuroimaging analysis software | ||
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| #### SPM | ||
| * [website](https://www.fil.ion.ucl.ac.uk/spm/) | ||
| * [manual](https://www.fil.ion.ucl.ac.uk/spm/doc/) | ||
| * [mailing list](https://www.fil.ion.ucl.ac.uk/spm/support/) | ||
| * [course/tutorial](http://www.fil.ion.ucl.ac.uk/spm/course/) | ||
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| #### Freesurfer | ||
| * [website](https://surfer.nmr.mgh.harvard.edu/) | ||
| * [manual](https://surfer.nmr.mgh.harvard.edu/fswiki) | ||
| * [mailing list](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSupport) | ||
| * [course](https://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA) and [videos](https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription) | ||
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| #### FSL | ||
| * [website](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) | ||
| * [manual](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Support) | ||
| * [mailing list](https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl) | ||
| * [course/tutorial](https://fsl.fmrib.ox.ac.uk/fslcourse/) | ||
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| #### AFNI | ||
| * [website](https://afni.nimh.nih.gov/) | ||
| * [manual](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/index.html) | ||
| * [mailing list](https://afni.nimh.nih.gov/afni/community/board/list.php?1) | ||
| * course/tutorial: Video recordings from the [AFNI bootcamp](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/educational/bootcamp_recordings.html), with slides, and [example data](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/unix_tutorial/misc/install.data.html). | ||
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| #### ANTs | ||
| * [website](http://stnava.github.io/ANTs/) | ||
| * [manual/wiki](https://github.com/ANTsX/ANTs/wiki) | ||
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| #### Nipype | ||
| Nipype is best viewed as a way to create and run software-agnostic preprocessing/analysis-pipeline. It becomes very powerful when you need to use different softwares in your analysis. | ||
| * [website](https://nipype.readthedocs.io/en/latest/) | ||
| * [course/tutorial](https://miykael.github.io/nipype_tutorial/) | ||
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| #### Dipy | ||
| Diffusion neuroimaging in Python | ||
| * [website](https://github.com/ohbm/hackathon2019) | ||
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| #### MRtrix3 | ||
| Advanced tools for the analysis of diffusion MRI data | ||
| * [website](http://www.mrtrix.org/) | ||
| * [community forum](http://community.mrtrix.org/) | ||
| * [user documentation](https://mrtrix.readthedocs.io/en/latest/) | ||
| * [developer documentation](http://www.mrtrix.org/developer-documentation/) | ||
| * [manuscript preprint](https://www.biorxiv.org/content/10.1101/551739v1). Includes example code for both C++11 and Python libraries. | ||
| * [BATMAN tutorial](https://osf.io/fkyht/). MRtrix3 tutorial available on OSF with an awesome title: B.A.T.M.A.N., the Basic and Advanced Tractography with MRtrix for All Neurophiles |