awesome-awesomeness/terminal/neuroimaging

                                                                                  Awesome Neuroimaging !Awesome (https://awesome.re/badge.svg) (https://awesome.re)

▐ Exploring, organizing, and analysing brain images and recordings. MR focused.

Contents

- Viewers (#viewers)
- Acquisition (#acquisition)
  - MR (#mr)
- Quality Assurance and Checking (#quality-assurance-and-checking)
- Pipelines (#pipelines)
  - Suites (#suites)
  - BOLD (#bold)
  - DSI (#dsi)
  - Structural (#structural)
- Raw Data (#raw-data)
- Provenance and Automation (#provenance-and-automation) 
- Imaging Tools (#imaging-tools)
  - Skullstripping (#skullstripping)
  - Warping (#warping)
  - Manipulation (#manipulation)
  - Modeling (#modeling)
- Libraries (#libraries)
- Resources (#resources)
  - Blogs, Books, and Docs (#blogs-books-and-docs)
  - Boards And Chats (#boards-and-chats)
  - Datasets Repositories (#datasets-repositories)


Viewers
- AFNI (https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/gui_guide/main_toc.html) - Volumetric viewer from the AFNI suit. GUI's aesthetic defined by the '90s era Motif toolkit.
- freeview (https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction) - Surface and volumetric image viewer in Freesurfer suit. Uses the QT toolkit.
- fsleyes (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes) - Volumetric viewer from FSL.
- mricron (https://www.nitrc.org/projects/mricron) - Volumetric viewer that works on windows.
- dsistudio (https://dsi-studio.labsolver.org/doc/gui_t1.html) - DSI viewer from the dsi-studio suit of tools.
- osirix (https://www.osirix-viewer.com/) - DICOM database organizer and viewer.
- Mango (https://mangoviewer.com/) - Multi-image Analysis GUI is a viewer for medical research images for dcm, nii, surface, etc; version 4.1 released in 2019.
- wb_view (https://www.humanconnectome.org/software/connectome-workbench) - Connectome workbench surface file viewer.

Acquisition
MR
Organization
- reproIn (https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html) - Naming exam card sequences.
- BIDS (https://bids-specification.readthedocs.io/en/stable/) - Brain Imaging Data Structure - directory hierarchy and file naming specification.
Management
- PACS (https://en.wikipedia.org/wiki/Picture_archiving_and_communication_system) - Picture Archiving and Communication System standard used to store and transfer DICOM images from medical equipment and likely implemented by scanner manufacture. 
See Siemens Healthineers Syngo Carbon (https://www.siemens-healthineers.com/en-us/digital-health-solutions/syngo-carbon), Phillips Vue PACS (https://www.documents.philips.com/assets/20240227/5a788a79bbdd4e1986f1b12300b0e534.pdf), GE HealthCare 
True PACS (https://www.gehealthcare.com/products/healthcare-it/true-pacs).
- XNAT (https://www.xnat.org/) - An extensible open-source imaging informatics software platform dedicated to imaging-based research.
  - DAX (https://github.com/VUIIS/dax) - Distributed Automation for XNAT: use containerization w/YAML defined input/output.
- LORIS (https://mcin.ca/technology/loris/) - LORIS (Longitudinal Online Research and Imaging System) is web-based data and project management software for neuroimaging research studies.
- brainlife.io (https://brainlife.io) - Open-source, free and secure reproducible neuroscience analysis platform.
- cbrain (https://mcin.ca/technology/cbrain/) - CBRAIN is web-based software that allows neuroimaging researchers to perform computationally intensive analyses on data by connecting them to High-Performance Computing (HPC).
- 💲Flywheel (https://flywheel.io) - A cloud-based imaging research data platform for data capture, curating, automation, and machine learning.
- 💲QMENTA (https://qmenta.com) - The all in one imaging platform for your clinical trial.

Motion
- FIRMM (https://firmm.readthedocs.io) - Real-time motion monitoring for fMRI, diffusion, and navigated T1/T2 image acquisition. 
- Dimon (https://afni.nimh.nih.gov/pub/dist/doc/program_help/Dimon.html) - Monitor real-time acquisition of DICOM image files with AFNI.


Quality Assurance and Checking

QA and QC of scanner images.

- MRIQC (https://mriqc.readthedocs.io/) - Extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data.
- mrQA (https://github.com/Open-Minds-Lab/mrQA) - Tools for quality assurance in medical imaging datasets, including protocol compliance.
- bids-validator (https://github.com/bids-standard/bids-validator/) - Validator for the Brain Imaging Data Structure.

Pipelines

Preprocessing workflows.

Suites
Software packages for multiple modalities, often offering a graphical user interface.


- AFNI (https://afni.nimh.nih.gov/) - 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.
- FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) - A comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data.
- SPM (https://www.fil.ion.ucl.ac.uk/spm/) - Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.
- Qu|Nex (https://qunex.yale.edu/) - The Quantitative Neuroimaging Environment & 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.



BOLD

- fmriprep (https://fmriprep.org/) - Accessible preprocessing pipeline robust to variations in scan acquisition protocols with comprehensive error and output reporting. Input is BIDS dataset.
- afni_proc.py (https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html) - Best practice pipelines with pre-configured blocks using AFNI.
- HALFpipe (https://github.com/HALFpipe/HALFpipe) - User-friendly software that facilitates reproducible analysis of fMRI data.
- XCP-D (https://xcp-d.readthedocs.io/en/latest/) - Post-processing and noise regression pipeline picks up right where fMRIprep ends.
- clpipe (https://clpipe.readthedocs.io/en/latest/) - 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.
- fmri_processing_scripts (https://github.com/LabNeuroCogDevel/fmri_processing_scripts) - Legacy pipeline for maximal preprocessing.
- HCP Pipeline (https://www.humanconnectome.org/software/hcp-mr-pipelines) - Pipeline scripts implement the Minimal Preprocessing Pipeline (MPP) described in Glasser et al. 2013 (http://www.ncbi.nlm.nih.gov/pubmed/23668970).

DSI

- dsi-studio (https://dsi-studio.labsolver.org/) - A tractography software tool that maps brain connections and correlates findings with neuropsychological disorders.
- qsiprep (https://qsiprep.readthedocs.io/) - Configures pipelines for processing diffusion-weighted MRI (dMRI) data.

Structural

- Freesurfer (https://freesurfer.net/) - An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images.
- CIVET (https://mcin.ca/technology/civet/) - An image processing pipeline for fully automated volumetric, corticometric, and morphometric analysis of human brain imaging data.


Raw Data

Dealing with DICOM and k-space images

- dcm2niix (https://github.com/rordenlab/dcm2niix) - DICOM to NIfTI converter.
- heudiconv (https://github.com/nipy/heudiconv/) - A flexible DICOM converter for organizing brain imaging data into structured directory layouts.
- gdcm (https://sourceforge.net/projects/gdcm/) - Grassroots DICOM is a  C++ library and CLI tool for DICOM medical files.
- pydicom (https://pydicom.github.io/) - Python package and cli tool for inspecting, modifying, and creating DICOM files.
- dicom_hinfo (https://afni.nimh.nih.gov/pub/dist/doc/program_help/dicom_hinfo.html), dicom_hdr - Prints selected information from the DICOM file.

- dcmdirtab, dcmtab_bids (https://lncd.github.io/lncdtools/BIDS/) - CLI focused, regular expression based, and iteration friendly BIDS conversion pipeline from lncdtools (https://github.com/lncd/lncdtools/).
- pymapVBVD (https://git.fmrib.ox.ac.uk/wclarke/pymapvbvd) - Reads Siemens .dat 'twix' raw data files. Python port of Philipp Ehses' Matlab tool mapVBVD.
- med2image (https://github.com/FNNDSC/med2image/pulls) - Python CLI tool for generating jpg or png images from DICOM or nifti files.

Provenance and Automation

- make (https://www.frontiersin.org/articles/10.3389/fninf.2016.00002/full) - follow script recipes defined in Makefile.
- datalad (https://github.com/datalad/datalad) - Keep code, data, containers under control with git and git-annex. Esp datalad run --input=... --output=....
- 3dNotes (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dNotes.html) - A program to add, delete and show notes for AFNI datasets. 

- niinote (https://github.com/lncd/lncdtools/blob/master/niinote) - Add AFNI nifti XML history to header to run and record any command. Part of lncdtools (https://github.com/lncd/lncdtools/).

Imaging Tools
Software to read, write, and manipulate volumetric and/or surface data.

Skullstripping
- optibet (https://montilab.psych.ucla.edu/fmri-wiki/optibet/) - Shell script to combine afni and fsl tools for more robust skull stripping in patient populations.

- 3dSkullStrip (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dSkullStrip.html) - AFNI (https://afni.nimh.nih.gov/)'s skull stripping utility with many parameters.

- bet (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/BET/UserGuide) - FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)'s brain extraction tool.

- antsBrainExtraction.sh (https://dpaniukov.github.io/2016/06/06/brain-extraction-with-ants.html)  - ANTs (http://stnava.github.io/ANTs/) version.

- mri-watershed (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed) - Part of the Freesurfer (https://freesurfer.net/) pipeline.
- ROBEX (https://www.nitrc.org/projects/robex) - Robust Brain Extraction without parameter tweaking.

Warping
Spatial normalization


- ANTs (http://stnava.github.io/ANTs/) - 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.

- 3dQwarp (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html) - OpenMP parallelized AFNI (https://afni.nimh.nih.gov/) tool to compute a nonlinearly warped version of source dataset to match a base dataset.

- flirt, fnirt (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT/UserGuide) - Warping software provided by FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) tools.

Templates
- templateflow (https://www.templateflow.org/) - A modular, version-controlled resource that allows researchers to use templates "off-the-shelf" and share new ones.
- MNI152 (https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) - Unbiased standard magnetic resonance imaging template brain volume for normal population.

Manipulation
Tools for doing math on matrix values

- 3dcalc (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dcalc.html) - Voxel-by-voxel arithmetic on 1D to 4D datasets. From AFNI.
- fslmaths (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils#:~:text=a%20combined%20image.-,fslmaths,--%20simple%20but%20powerful) - Simple but powerful program to allow mathematical manipulation of images. From FSL.
- fscalc (https://www.freesurfer.net/pub/dist/freesurfer/dev_binaries/centos6_x86_64/fscalc.fsl) - Freesurfer wrapper of fslmaths.



Modeling

HRF


- 3dDeconvolve (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDeconvolve.html) -  AFNI (https://afni.nimh.nih.gov/) - 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.

- FEAT (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT) - GUI guided analysis of simple experiment based on general linear modeling. Part of FSL (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki).

MRSI

- lcmodel (https://github.com/schorschinho/LCModel) - Implements linear-combination modeling of magnetic resonance spectroscopy data.
- FSL-MRS (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSL-MRS) - A suite of tools for MR Spectroscopy, including single voxel (SVS), MRS imaging (MRSI), functional MRS (fMRS), diffusion MRS (dwMRS), edited spectroscopy, etc.
- Osprey (https://github.com/schorschinho/osprey) - An all-in-one software suite for state-of-the art processing and quantitative analysis of in-vivo magnetic resonance spectroscopy (MRS) data.

EEG
- fooof (https://fooof-tools.github.io/fooof/index.html) -  Fast, efficient, and physiologically-informed tool to parameterize neural power spectra.

Misc
- hurst (https://github.com/elifesciences-publications/ei_hurst/) - Algorithm to assess intrinsic excitation-inhibition imbalance in MR (Trakoshis et al, eLife, 2020 (http://doi.org/10.7554/eLife.55684)).

- tat2 (https://lncd.github.io/lncdtools/tat2/) - Time-averaged T2 wrapper script using AFNI binaries from lncdtools (https://github.com/lncd/lncdtools/).

Libraries

Python

- nipy (https://nipy.org/) - Includes nibabel, nipype, and nilearn.

R
- oro.nifti (https://github.com/bjw34032/oro.nifti) - Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.

MATLAB


- SPM (https://www.fil.ion.ucl.ac.uk/spm/) - Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.
- imtool3D_td (https://github.com/tanguyduval/imtool3D_td) - 3D Image Viewer with ROI tools for Matlab (NIFTI viewer, Manual segmentation).

Resources

Blogs, Books, and Docs

- Andy's brain blog (https://andysbrainblog.com/) - Tutorials and videos about neuroimaging analysis from start to finish in all the major software packages (AFNI, SPM, and FSL).
- DataLad handbook (https://handbook.datalad.org/) - Start-to-end use cases of specific applications in neuroimaging using provenance tracking software datalad.
- Hitchhacker's guide to the brain (https://learn-neuroimaging.github.io/hitchhackers_guide_brain/) - Notes from study planning to reporting and data sharing by way of acquisition, processing, analysis, and quality control.
- Online Neuroimaging Resources (https://github.com/Remi-Gau/online_neuroimaging_resources) - A laundry list of online resources for MRI, fMRI, EEG, MEG.
- U of A: Neuroimaging Core Documentation (https://neuroimaging-core-docs.readthedocs.io/) - Documentation for approaches used and/or developed by the neuroimaging core at the University of Arizona.

Boards And Chats
- neurostars (https://neurostars.org/) - General neuroimaging discuss form. fmriprep suggested Q&A site.
- afni discuss (https://discuss.afni.nimh.nih.gov) - AFNI's discuss instance.
- brainhack (https://mattermost.brainhack.org/) - A mattermoust community of neuroimagers.

Datasets Repositories

- openneuro (https://openneuro.org/) - A free and open platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG, and iEEG data.
- NDA (https://nda.nih.gov/) - National Institute of Mental Health Data Archive (NDA) makes available human subjects data collected from hundreds of research projects across many scientific domains.
- NITRC (https://www.nitrc.org/) - NeuroImaging Tools & Resources Collaboratory library of neuroinformatics software and data. 

Big datasets

- ABCD (https://abcdstudy.org/) - Long-term Adolescent Brain Cognitive Development study including 1000s of longitudinal MRI scans.
- UK Biobank (https://www.ukbiobank.ac.uk/) -  A large-scale biomedical database and research resource with 500,000 research participants.
- NCANDA (http://www.ncanda.org/) - National Consortium on Alcohol and Neurodevelopment in Adolescence (4000+ MR visits).
- PNC (https://www.med.upenn.edu/bbl/philadelphianeurodevelopmentalcohort.html) -  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.
- ENIGMA (https://enigma.ini.usc.edu/) - The Enhancing Neuro Imaging Genetics through Meta Analysis Consortium contains 50 working group's imaging and genomics data.

Contributing

Contributions welcome! Read the contribution guidelines (contributing.md) first.

neuroimaging Github: https://github.com/NPACore/awesome-neuroimaging