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<h1 id="awesome-neuroimaging-awesome">Awesome Neuroimaging <a
href="https://awesome.re"><img src="https://awesome.re/badge.svg"
alt="Awesome" /></a></h1>
<blockquote>
<p>Exploring, organizing, and analysing brain images and recordings. MR
focused.</p>
</blockquote>
<h2 id="contents">Contents</h2>
<ul>
<li><a href="#viewers">Viewers</a></li>
<li><a href="#acquisition">Acquisition</a>
<ul>
<li><a href="#mr">MR</a></li>
</ul></li>
<li><a href="#quality-assurance-and-checking">Quality Assurance and
Checking</a></li>
<li><a href="#pipelines">Pipelines</a>
<ul>
<li><a href="#suites">Suites</a></li>
<li><a href="#bold">BOLD</a></li>
<li><a href="#dsi">DSI</a></li>
<li><a href="#structural">Structural</a></li>
</ul></li>
<li><a href="#raw-data">Raw Data</a></li>
<li><a href="#provenance-and-automation">Provenance and
Automation</a></li>
<li><a href="#imaging-tools">Imaging Tools</a>
<ul>
<li><a href="#skullstripping">Skullstripping</a></li>
<li><a href="#warping">Warping</a></li>
<li><a href="#manipulation">Manipulation</a></li>
<li><a href="#modeling">Modeling</a></li>
</ul></li>
<li><a href="#libraries">Libraries</a></li>
<li><a href="#resources">Resources</a>
<ul>
<li><a href="#blogs-books-and-docs">Blogs, Books, and Docs</a></li>
<li><a href="#boards-and-chats">Boards And Chats</a></li>
<li><a href="#datasets-repositories">Datasets Repositories</a></li>
</ul></li>
</ul>
<h2 id="viewers">Viewers</h2>
<ul>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/gui_guide/main_toc.html">AFNI</a>
- Volumetric viewer from the AFNI suit. GUI’s aesthetic defined by the
’90s era Motif toolkit.</li>
<li><a
href="https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction">freeview</a>
- Surface and volumetric image viewer in Freesurfer suit. Uses the QT
toolkit.</li>
<li><a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes">fsleyes</a>
- Volumetric viewer from FSL.</li>
<li><a href="https://www.nitrc.org/projects/mricron">mricron</a> -
Volumetric viewer that works on windows.</li>
<li><a
href="https://dsi-studio.labsolver.org/doc/gui_t1.html">dsistudio</a> -
DSI viewer from the dsi-studio suit of tools.</li>
<li><a href="https://www.osirix-viewer.com/">osirix</a> - DICOM database
organizer and viewer.</li>
<li><a href="https://mangoviewer.com/">Mango</a> - Multi-image Analysis
GUI is a viewer for medical research images for dcm, nii, surface, etc;
version 4.1 released in 2019.</li>
<li><a
href="https://www.humanconnectome.org/software/connectome-workbench"><code>wb_view</code></a>
- Connectome workbench surface file viewer.</li>
</ul>
<h2 id="acquisition">Acquisition</h2>
<h3 id="mr">MR</h3>
<h4 id="organization">Organization</h4>
<ul>
<li><a
href="https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html">reproIn</a>
- Naming exam card sequences.</li>
<li><a
href="https://bids-specification.readthedocs.io/en/stable/">BIDS</a> -
Brain Imaging Data Structure - directory hierarchy and file naming
specification. #### Management</li>
<li><a
href="https://en.wikipedia.org/wiki/Picture_archiving_and_communication_system">PACS</a>
- Picture Archiving and Communication System standard used to store and
transfer DICOM images from medical equipment and likely implemented by
scanner manufacture. See <a
href="https://www.siemens-healthineers.com/en-us/digital-health-solutions/syngo-carbon">Siemens
Healthineers Syngo Carbon</a>, <a
href="https://www.documents.philips.com/assets/20240227/5a788a79bbdd4e1986f1b12300b0e534.pdf">Phillips
Vue PACS</a>, <a
href="https://www.gehealthcare.com/products/healthcare-it/true-pacs">GE
HealthCare True PACS</a>.</li>
<li><a href="https://www.xnat.org/">XNAT</a> - An extensible open-source
imaging informatics software platform dedicated to imaging-based
research.
<ul>
<li><a href="https://github.com/VUIIS/dax">DAX</a> - Distributed
Automation for XNAT: use containerization w/YAML defined
input/output.</li>
</ul></li>
<li><a href="https://mcin.ca/technology/loris/">LORIS</a> - LORIS
(Longitudinal Online Research and Imaging System) is web-based data and
project management software for neuroimaging research studies.</li>
<li><a href="https://brainlife.io">brainlife.io</a> - Open-source, free
and secure reproducible neuroscience analysis platform.</li>
<li><a href="https://mcin.ca/technology/cbrain/">cbrain</a> - CBRAIN is
web-based software that allows neuroimaging researchers to perform
computationally intensive analyses on data by connecting them to
High-Performance Computing (HPC).</li>
<li>💲<a href="https://flywheel.io">Flywheel</a> - A cloud-based imaging
research data platform for data capture, curating, automation, and
machine learning.</li>
<li>💲<a href="https://qmenta.com">QMENTA</a> - The all in one imaging
platform for your clinical trial.</li>
</ul>
<h4 id="motion">Motion</h4>
<ul>
<li><a href="https://firmm.readthedocs.io">FIRMM</a> - Real-time motion
monitoring for fMRI, diffusion, and navigated T1/T2 image
acquisition.</li>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/Dimon.html"><code>Dimon</code></a>
- Monitor real-time acquisition of DICOM image files with AFNI.</li>
</ul>
<h2 id="quality-assurance-and-checking">Quality Assurance and
Checking</h2>
<p>QA and QC of scanner images.</p>
<ul>
<li><a href="https://mriqc.readthedocs.io/">MRIQC</a> - Extracts
no-reference IQMs (image quality metrics) from structural (T1w and T2w)
and functional MRI (magnetic resonance imaging) data.</li>
<li><a href="https://github.com/Open-Minds-Lab/mrQA">mrQA</a> - Tools
for quality assurance in medical imaging datasets, including protocol
compliance.</li>
<li><a
href="https://github.com/bids-standard/bids-validator/">bids-validator</a>
- Validator for the Brain Imaging Data Structure.</li>
</ul>
<h2 id="pipelines">Pipelines</h2>
<p>Preprocessing workflows.</p>
<h3 id="suites">Suites</h3>
<p>Software packages for multiple modalities, often offering a graphical
user interface.</p>
<!--lint ignore double-link-->
<ul>
<li><a href="https://afni.nimh.nih.gov/">AFNI</a> - Analysis of
Functional NeuroImages is a leading software suite of C, Python, R
programs and shell scripts primarily developed for the analysis and
display of multiple MRI modalities.</li>
<li><a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki">FSL</a> - A
comprehensive library of analysis tools for FMRI, MRI and diffusion
brain imaging data.</li>
<li><a href="https://www.fil.ion.ucl.ac.uk/spm/">SPM</a> - Statistical
Parametric Mapping refers to the construction and assessment of
spatially extended statistical processes used to test hypotheses about
functional imaging data.</li>
<li><a href="https://qunex.yale.edu/">Qu|Nex</a> - The Quantitative
Neuroimaging Environment &amp; Toolbox (QuNex) is an open-source
software suite that collectively supports an extensible framework for
data organization, preprocessing, quality assurance, and analyses across
neuroimaging modalities.
<!-- - [MINC](https://mcin.ca/technology/minc/) -- more of a format than suit? --></li>
</ul>
<h3 id="bold">BOLD</h3>
<ul>
<li><a href="https://fmriprep.org/">fmriprep</a> - Accessible
preprocessing pipeline robust to variations in scan acquisition
protocols with comprehensive error and output reporting. Input is BIDS
dataset.</li>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html"><code>afni_proc.py</code></a>
- Best practice pipelines with pre-configured blocks using AFNI.</li>
<li><a href="https://github.com/HALFpipe/HALFpipe">HALFpipe</a> -
User-friendly software that facilitates reproducible analysis of fMRI
data.</li>
<li><a href="https://xcp-d.readthedocs.io/en/latest/">XCP-D</a> -
Post-processing and noise regression pipeline picks up right where
fMRIprep ends.</li>
<li><a href="https://clpipe.readthedocs.io/en/latest/">clpipe</a> - Uses
fmriprep for preprocessing fMRI data and implements a variety of
additional processing steps important for functional connectivity
analyses such as nuisance regression and filtering.</li>
<li><a
href="https://github.com/LabNeuroCogDevel/fmri_processing_scripts">fmri_processing_scripts</a>
- Legacy pipeline for maximal preprocessing.</li>
<li><a
href="https://www.humanconnectome.org/software/hcp-mr-pipelines">HCP
Pipeline</a> - Pipeline scripts implement the Minimal Preprocessing
Pipeline (MPP) described in <a
href="http://www.ncbi.nlm.nih.gov/pubmed/23668970">Glasser et
al. 2013</a>.</li>
</ul>
<h3 id="dsi">DSI</h3>
<ul>
<li><a href="https://dsi-studio.labsolver.org/">dsi-studio</a> - A
tractography software tool that maps brain connections and correlates
findings with neuropsychological disorders.</li>
<li><a href="https://qsiprep.readthedocs.io/">qsiprep</a> - Configures
pipelines for processing diffusion-weighted MRI (dMRI) data.</li>
</ul>
<h3 id="structural">Structural</h3>
<!--lint ignore double-link-->
<ul>
<li><a href="https://freesurfer.net/">Freesurfer</a> - An open source
neuroimaging toolkit for processing, analyzing, and visualizing human
brain MR images.</li>
<li><a href="https://mcin.ca/technology/civet/">CIVET</a> - An image
processing pipeline for fully automated volumetric, corticometric, and
morphometric analysis of human brain imaging data.</li>
</ul>
<h2 id="raw-data">Raw Data</h2>
<p>Dealing with DICOM and k-space images</p>
<ul>
<li><a href="https://github.com/rordenlab/dcm2niix">dcm2niix</a> - DICOM
to NIfTI converter.</li>
<li><a href="https://github.com/nipy/heudiconv/">heudiconv</a> - A
flexible DICOM converter for organizing brain imaging data into
structured directory layouts.</li>
<li><a href="https://sourceforge.net/projects/gdcm/">gdcm</a> -
Grassroots DICOM is a C++ library and CLI tool for DICOM medical
files.</li>
<li><a href="https://pydicom.github.io/"><code>pydicom</code></a> -
Python package and cli tool for inspecting, modifying, and creating
DICOM files.</li>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/dicom_hinfo.html"><code>dicom_hinfo</code></a>,
<code>dicom_hdr</code> - Prints selected information from the DICOM
file. <!--lint ignore double-link--></li>
<li><a
href="https://lncd.github.io/lncdtools/BIDS/"><code>dcmdirtab</code>,
<code>dcmtab_bids</code></a> - CLI focused, regular expression based,
and iteration friendly BIDS conversion pipeline from <a
href="https://github.com/lncd/lncdtools/">lncdtools</a>.</li>
<li><a href="https://git.fmrib.ox.ac.uk/wclarke/pymapvbvd">pymapVBVD</a>
- Reads Siemens .dat ‘twix’ raw data files. Python port of Philipp
Ehses’ Matlab tool mapVBVD.</li>
<li><a href="https://github.com/FNNDSC/med2image/pulls">med2image</a> -
Python CLI tool for generating jpg or png images from DICOM or nifti
files.</li>
</ul>
<h2 id="provenance-and-automation">Provenance and Automation</h2>
<ul>
<li><a
href="https://www.frontiersin.org/articles/10.3389/fninf.2016.00002/full">make</a>
- follow script recipes defined in <code>Makefile</code>.</li>
<li><a href="https://github.com/datalad/datalad">datalad</a> - Keep
code, data, containers under control with git and git-annex. Esp
<code>datalad run --input=... --output=...</code>.</li>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dNotes.html"><code>3dNotes</code></a>
- A program to add, delete and show notes for AFNI datasets.
<!--lint ignore double-link--></li>
<li><a
href="https://github.com/lncd/lncdtools/blob/master/niinote"><code>niinote</code></a>
- Add AFNI nifti XML history to header to run and record any command.
Part of <a href="https://github.com/lncd/lncdtools/">lncdtools</a>.</li>
</ul>
<h2 id="imaging-tools">Imaging Tools</h2>
<p>Software to read, write, and manipulate volumetric and/or surface
data.</p>
<h3 id="skullstripping">Skullstripping</h3>
<ul>
<li><a
href="https://montilab.psych.ucla.edu/fmri-wiki/optibet/">optibet</a> -
Shell script to combine afni and fsl tools for more robust skull
stripping in patient populations. <!--lint ignore double-link--></li>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSkullStrip.html"><code>3dSkullStrip</code></a>
- <a href="https://afni.nimh.nih.gov/">AFNI</a>’s skull stripping
utility with many parameters. <!--lint ignore double-link--></li>
<li><a
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide"><code>bet</code></a>
- <a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki">FSL</a>’s brain
extraction tool. <!--lint ignore double-link--></li>
<li><a
href="https://dpaniukov.github.io/2016/06/06/brain-extraction-with-ants.html"><code>antsBrainExtraction.sh</code></a>
- <a href="http://stnava.github.io/ANTs/">ANTs</a> version.
<!--lint ignore double-link--></li>
<li><a
href="https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed"><code>mri-watershed</code></a>
- Part of the <a href="https://freesurfer.net/">Freesurfer</a>
pipeline.</li>
<li><a href="https://www.nitrc.org/projects/robex">ROBEX</a> - Robust
Brain Extraction without parameter tweaking.</li>
</ul>
<h3 id="warping">Warping</h3>
<p>Spatial normalization</p>
<!--lint ignore double-link-->
<ul>
<li><a href="http://stnava.github.io/ANTs/">ANTs</a> - Advanced
Normalization Tools includes probabilistic tissue segmentation and
machine learning methods based on expert labeled data to order to
maximize reliability and consistency of multiple modality image
segmentation. <!--lint ignore double-link--></li>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html">3dQwarp</a>
- OpenMP parallelized <a href="https://afni.nimh.nih.gov/">AFNI</a> tool
to compute a nonlinearly warped version of source dataset to match a
base dataset. <!--lint ignore double-link--></li>
<li><a
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT/UserGuide">flirt,
fnirt</a> - Warping software provided by <a
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki">FSL</a> tools.</li>
</ul>
<h4 id="templates">Templates</h4>
<ul>
<li><a href="https://www.templateflow.org/">templateflow</a> - A
modular, version-controlled resource that allows researchers to use
templates “off-the-shelf” and share new ones.</li>
<li><a
href="https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009">MNI152</a>
- Unbiased standard magnetic resonance imaging template brain volume for
normal population.</li>
</ul>
<h3 id="manipulation">Manipulation</h3>
<p>Tools for doing math on matrix values</p>
<ul>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dcalc.html">3dcalc</a>
- Voxel-by-voxel arithmetic on 1D to 4D datasets. From AFNI.</li>
<li><a
href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils#:~:text=a%20combined%20image.-,fslmaths,--%20simple%20but%20powerful">fslmaths</a>
- Simple but powerful program to allow mathematical manipulation of
images. From FSL.</li>
<li><a
href="https://www.freesurfer.net/pub/dist/freesurfer/dev_binaries/centos6_x86_64/fscalc.fsl">fscalc</a>
- Freesurfer wrapper of fslmaths.
<!--- Also see [#Libraries](#libraries) for development interfaces to be used within programming language.--></li>
</ul>
<h3 id="modeling">Modeling</h3>
<h4 id="hrf">HRF</h4>
<!--lint ignore double-link-->
<ul>
<li><a
href="https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDeconvolve.html">3dDeconvolve</a>
- <a href="https://afni.nimh.nih.gov/">AFNI</a> - Program to calculate
the deconvolution of a measurement 3D+time dataset with a specified
input stimulus time series. This program can also perform multiple
linear regression using multiple input stimulus time series.
<!--lint ignore double-link--></li>
<li><a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT">FEAT</a> - GUI
guided analysis of simple experiment based on general linear modeling.
Part of <a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki">FSL</a>.</li>
</ul>
<h4 id="mrsi">MRSI</h4>
<ul>
<li><a href="https://github.com/schorschinho/LCModel">lcmodel</a> -
Implements linear-combination modeling of magnetic resonance
spectroscopy data.</li>
<li><a href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL-MRS">FSL-MRS</a>
- A suite of tools for MR Spectroscopy, including single voxel (SVS),
MRS imaging (MRSI), functional MRS (fMRS), diffusion MRS (dwMRS), edited
spectroscopy, etc.</li>
<li><a href="https://github.com/schorschinho/osprey">Osprey</a> - An
all-in-one software suite for state-of-the art processing and
quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS)
data.</li>
</ul>
<h4 id="eeg">EEG</h4>
<ul>
<li><a
href="https://fooof-tools.github.io/fooof/index.html"><code>fooof</code></a>
- Fast, efficient, and physiologically-informed tool to parameterize
neural power spectra.</li>
</ul>
<h4 id="misc">Misc</h4>
<ul>
<li><a
href="https://github.com/elifesciences-publications/ei_hurst/">hurst</a>
- Algorithm to assess intrinsic excitation-inhibition imbalance in MR
(<a href="http://doi.org/10.7554/eLife.55684">Trakoshis et al, eLife,
2020</a>). <!--lint ignore double-link--></li>
<li><a href="https://lncd.github.io/lncdtools/tat2/">tat2</a> -
Time-averaged T2* wrapper script using AFNI binaries from <a
href="https://github.com/lncd/lncdtools/">lncdtools</a>.</li>
</ul>
<h2 id="libraries">Libraries</h2>
<h3 id="python">Python</h3>
<ul>
<li><a href="https://nipy.org/">nipy</a> - Includes
<code>nibabel</code>, <code>nipype</code>, and
<code>nilearn</code>.</li>
</ul>
<h3 id="r">R</h3>
<ul>
<li><a href="https://github.com/bjw34032/oro.nifti">oro.nifti</a> -
Functions for the input/output and visualization of medical imaging data
that follow either the ANALYZE, NIfTI or AFNI formats.</li>
</ul>
<h3 id="matlab">MATLAB</h3>
<!--lint ignore double-link-->
<ul>
<li><a href="https://www.fil.ion.ucl.ac.uk/spm/">SPM</a> - Statistical
Parametric Mapping refers to the construction and assessment of
spatially extended statistical processes used to test hypotheses about
functional imaging data.</li>
<li><a
href="https://github.com/tanguyduval/imtool3D_td"><code>imtool3D_td</code></a>
- 3D Image Viewer with ROI tools for Matlab (NIFTI viewer, Manual
segmentation).</li>
</ul>
<h2 id="resources">Resources</h2>
<h3 id="blogs-books-and-docs">Blogs, Books, and Docs</h3>
<ul>
<li><a href="https://andysbrainblog.com/">Andy’s brain blog</a> -
Tutorials and videos about neuroimaging analysis from start to finish in
all the major software packages (AFNI, SPM, and FSL).</li>
<li><a href="https://handbook.datalad.org/">DataLad handbook</a> -
Start-to-end use cases of specific applications in neuroimaging using
provenance tracking software <code>datalad</code>.</li>
<li><a
href="https://learn-neuroimaging.github.io/hitchhackers_guide_brain/">Hitchhacker’s
guide to the brain</a> - Notes from study planning to reporting and data
sharing by way of acquisition, processing, analysis, and quality
control.</li>
<li><a
href="https://github.com/Remi-Gau/online_neuroimaging_resources">Online
Neuroimaging Resources</a> - A laundry list of online resources for MRI,
fMRI, EEG, MEG.</li>
<li><a href="https://neuroimaging-core-docs.readthedocs.io/">U of A:
Neuroimaging Core Documentation</a> - Documentation for approaches used
and/or developed by the neuroimaging core at the University of
Arizona.</li>
</ul>
<h3 id="boards-and-chats">Boards And Chats</h3>
<ul>
<li><a href="https://neurostars.org/">neurostars</a> - General
neuroimaging <code>discuss</code> form. <code>fmriprep</code> suggested
Q&amp;A site.</li>
<li><a href="https://discuss.afni.nimh.nih.gov">afni discuss</a> -
AFNI’s <code>discuss</code> instance.</li>
<li><a href="https://mattermost.brainhack.org/">brainhack</a> - A
mattermoust community of neuroimagers.</li>
</ul>
<h3 id="datasets-repositories">Datasets Repositories</h3>
<ul>
<li><a href="https://openneuro.org/">openneuro</a> - A free and open
platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG,
and iEEG data.</li>
<li><a href="https://nda.nih.gov/">NDA</a> - National Institute of
Mental Health Data Archive (NDA) makes available human subjects data
collected from hundreds of research projects across many scientific
domains.</li>
<li><a href="https://www.nitrc.org/">NITRC</a> - NeuroImaging Tools
&amp; Resources Collaboratory library of neuroinformatics software and
data.</li>
</ul>
<h4 id="big-datasets">Big datasets</h4>
<ul>
<li><a href="https://abcdstudy.org/">ABCD</a> - Long-term Adolescent
Brain Cognitive Development study including 1000s of longitudinal MRI
scans.</li>
<li><a href="https://www.ukbiobank.ac.uk/">UK Biobank</a> - A
large-scale biomedical database and research resource with 500,000
research participants.</li>
<li><a href="http://www.ncanda.org/">NCANDA</a> - National Consortium on
Alcohol and Neurodevelopment in Adolescence (4000+ MR visits).</li>
<li><a
href="https://www.med.upenn.edu/bbl/philadelphianeurodevelopmentalcohort.html">PNC</a>
- A population-based sample of over 9500 individuals from the greater
Philadelphia area, ages 8-21 years who received medical care at the CHOP
network.</li>
<li><a href="https://enigma.ini.usc.edu/">ENIGMA</a> - The Enhancing
Neuro Imaging Genetics through Meta Analysis Consortium contains 50
working group’s imaging and genomics data.</li>
</ul>
<h2 id="contributing">Contributing</h2>
<p>Contributions welcome! Read the <a
href="contributing.md">contribution guidelines</a> first.</p>
<p><a
href="https://github.com/NPACore/awesome-neuroimaging">neuroimaging.md
Github</a></p>