Awesome Neuroimaging 
Exploring, organizing, and analysing brain images and recordings. MR
focused.
Contents
Viewers
- AFNI
- Volumetric viewer from the AFNI suit. GUI’s aesthetic defined by the
’90s era Motif toolkit.
- freeview
- Surface and volumetric image viewer in Freesurfer suit. Uses the QT
toolkit.
- fsleyes
- Volumetric viewer from FSL.
- mricron -
Volumetric viewer that works on windows.
- dsistudio -
DSI viewer from the dsi-studio suit of tools.
- osirix - DICOM database
organizer and viewer.
- Mango - Multi-image Analysis
GUI is a viewer for medical research images for dcm, nii, surface, etc;
version 4.1 released in 2019.
wb_view
- Connectome workbench surface file viewer.
Acquisition
MR
Organization
- reproIn
- Naming exam card sequences.
- BIDS -
Brain Imaging Data Structure - directory hierarchy and file naming
specification. #### Management
- PACS
- 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, Phillips
Vue PACS, GE
HealthCare True PACS.
- XNAT - An extensible open-source
imaging informatics software platform dedicated to imaging-based
research.
- DAX - Distributed
Automation for XNAT: use containerization w/YAML defined
input/output.
- LORIS - LORIS
(Longitudinal Online Research and Imaging System) is web-based data and
project management software for neuroimaging research studies.
- brainlife.io - Open-source, free
and secure reproducible neuroscience analysis platform.
- 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 - A cloud-based imaging
research data platform for data capture, curating, automation, and
machine learning.
- 💲QMENTA - The all in one imaging
platform for your clinical trial.
Motion
- FIRMM - Real-time motion
monitoring for fMRI, diffusion, and navigated T1/T2 image
acquisition.
Dimon
- Monitor real-time acquisition of DICOM image files with AFNI.
Quality Assurance and
Checking
QA and QC of scanner images.
- MRIQC - Extracts
no-reference IQMs (image quality metrics) from structural (T1w and T2w)
and functional MRI (magnetic resonance imaging) data.
- mrQA - Tools
for quality assurance in medical imaging datasets, including protocol
compliance.
- 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 - 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 - A
comprehensive library of analysis tools for FMRI, MRI and diffusion
brain imaging data.
- 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 - 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 - Accessible
preprocessing pipeline robust to variations in scan acquisition
protocols with comprehensive error and output reporting. Input is BIDS
dataset.
afni_proc.py
- Best practice pipelines with pre-configured blocks using AFNI.- HALFpipe -
User-friendly software that facilitates reproducible analysis of fMRI
data.
- XCP-D -
Post-processing and noise regression pipeline picks up right where
fMRIprep ends.
- clpipe - 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
- Legacy pipeline for maximal preprocessing.
- HCP
Pipeline - Pipeline scripts implement the Minimal Preprocessing
Pipeline (MPP) described in Glasser et
al. 2013.
DSI
- dsi-studio - A
tractography software tool that maps brain connections and correlates
findings with neuropsychological disorders.
- qsiprep - Configures
pipelines for processing diffusion-weighted MRI (dMRI) data.
Structural
- Freesurfer - An open source
neuroimaging toolkit for processing, analyzing, and visualizing human
brain MR images.
- 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 - DICOM
to NIfTI converter.
- heudiconv - A
flexible DICOM converter for organizing brain imaging data into
structured directory layouts.
- gdcm -
Grassroots DICOM is a C++ library and CLI tool for DICOM medical
files.
pydicom -
Python package and cli tool for inspecting, modifying, and creating
DICOM files.dicom_hinfo,
dicom_hdr - Prints selected information from the DICOM
file. dcmdirtab,
dcmtab_bids - CLI focused, regular expression based,
and iteration friendly BIDS conversion pipeline from lncdtools.- pymapVBVD
- Reads Siemens .dat ‘twix’ raw data files. Python port of Philipp
Ehses’ Matlab tool mapVBVD.
- med2image -
Python CLI tool for generating jpg or png images from DICOM or nifti
files.
Provenance and Automation
- make
- follow script recipes defined in
Makefile.
- datalad - Keep
code, data, containers under control with git and git-annex. Esp
datalad run --input=... --output=....
3dNotes
- A program to add, delete and show notes for AFNI datasets.
niinote
- Add AFNI nifti XML history to header to run and record any command.
Part of lncdtools.
Software to read, write, and manipulate volumetric and/or surface
data.
Skullstripping
Warping
Spatial normalization
- 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
- OpenMP parallelized AFNI tool
to compute a nonlinearly warped version of source dataset to match a
base dataset.
- flirt,
fnirt - Warping software provided by FSL tools.
Templates
- templateflow - A
modular, version-controlled resource that allows researchers to use
templates “off-the-shelf” and share new ones.
- MNI152
- Unbiased standard magnetic resonance imaging template brain volume for
normal population.
Manipulation
Tools for doing math on matrix values
- 3dcalc
- Voxel-by-voxel arithmetic on 1D to 4D datasets. From AFNI.
- fslmaths
- Simple but powerful program to allow mathematical manipulation of
images. From FSL.
- fscalc
- Freesurfer wrapper of fslmaths.
Modeling
HRF
- 3dDeconvolve
- AFNI - 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 - GUI
guided analysis of simple experiment based on general linear modeling.
Part of FSL.
MRSI
- lcmodel -
Implements linear-combination modeling of magnetic resonance
spectroscopy data.
- 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 - 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
- Fast, efficient, and physiologically-informed tool to parameterize
neural power spectra.
Misc
Libraries
Python
- nipy - Includes
nibabel, nipype, and
nilearn.
R
- oro.nifti -
Functions for the input/output and visualization of medical imaging data
that follow either the ANALYZE, NIfTI or AFNI formats.
MATLAB
- 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
- 3D Image Viewer with ROI tools for Matlab (NIFTI viewer, Manual
segmentation).
Resources
Blogs, Books, and Docs
- Andy’s brain blog -
Tutorials and videos about neuroimaging analysis from start to finish in
all the major software packages (AFNI, SPM, and FSL).
- DataLad handbook -
Start-to-end use cases of specific applications in neuroimaging using
provenance tracking software
datalad.
- Hitchhacker’s
guide to the brain - Notes from study planning to reporting and data
sharing by way of acquisition, processing, analysis, and quality
control.
- Online
Neuroimaging Resources - A laundry list of online resources for MRI,
fMRI, EEG, MEG.
- U of A:
Neuroimaging Core Documentation - Documentation for approaches used
and/or developed by the neuroimaging core at the University of
Arizona.
Boards And Chats
- neurostars - General
neuroimaging
discuss form. fmriprep suggested
Q&A site.
- afni discuss -
AFNI’s
discuss instance.
- brainhack - A
mattermoust community of neuroimagers.
Datasets Repositories
- openneuro - A free and open
platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG,
and iEEG data.
- NDA - National Institute of
Mental Health Data Archive (NDA) makes available human subjects data
collected from hundreds of research projects across many scientific
domains.
- NITRC - NeuroImaging Tools
& Resources Collaboratory library of neuroinformatics software and
data.
Big datasets
- ABCD - Long-term Adolescent
Brain Cognitive Development study including 1000s of longitudinal MRI
scans.
- UK Biobank - A
large-scale biomedical database and research resource with 500,000
research participants.
- NCANDA - National Consortium on
Alcohol and Neurodevelopment in Adolescence (4000+ MR visits).
- PNC
- 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 - 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 first.
neuroimaging.md
Github