AFNI
Volumetric viewer from the AFNI suit. GUI's aesthetic defined by the '90s era Motif toolkit.
Volumetric viewer from the AFNI suit. GUI's aesthetic defined by the '90s era Motif toolkit.
Awesome Neuroimaging
Exploring, organizing, and analysing neuroimages (MR focus)
This page lists names, links and short descriptions. The original list on GitHub is the source and belongs to its authors.
Viewers
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
reproIn
Naming exam card sequences.
BIDS
Brain Imaging Data Structure - directory hierarchy and file naming specification.
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
Longitudinal Online Research and Imaging System is a web-based data and project management software for neuroimaging research studies.
brainlife.io
Open-source, free and secure reproducible neuroscience analysis platform.
cbrain
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.
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
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 >Suites
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.
In 2 lists
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.
Pipelines >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.
Pipelines >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.
Pipelines >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
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.
Imaging Tools >Skullstripping
optibet
Shell script to combine afni and fsl tools for more robust skull stripping in patient populations.
3dSkullStrip
AFNI's skull stripping utility with many parameters.
bet
FSL's brain extraction tool.
antsBrainExtraction.sh
ANTs version.
mri-watershed
Part of the Freesurfer pipeline.
ROBEX
Robust Brain Extraction without parameter tweaking.
Imaging Tools >Warping
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.
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.
Imaging Tools >Manipulation
Imaging Tools >Modeling
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.
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.
In 2 lists
fooof
Fast, efficient, and physiologically-informed tool to parameterize neural power spectra.
hurst
Algorithm to assess intrinsic excitation-inhibition imbalance in MR (Trakoshis et al, eLife, 2020).
tat2
Time-averaged T2* wrapper script using AFNI binaries from lncdtools.
Libraries >Python
nipy
Includes nibabel, nipype, and nilearn.
Libraries >R
oro.nifti
Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.
Libraries >MATLAB
SPM
Statistical Parametric Mapping refers to the construction and assessment of spatially extended statistical processes used to test hypotheses about functional imaging data.
In 2 lists
imtool3D_td
3D Image Viewer with ROI tools for Matlab (NIFTI viewer, Manual segmentation).
In 2 lists
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).
In 2 lists
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.
Resources >Boards And Chats
neurostars
General neuroimaging discuss form. fmriprep suggested Q&A site.
In 2 lists
afni discuss
AFNI's discuss instance.
brainhack
A mattermoust community of neuroimagers.
Resources >Datasets Repositories
openneuro
A free and open platform for validating and sharing BIDS-compliant MRI, PET, MEG, EEG, and iEEG data.
In 3 lists
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.
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.
In 2 lists
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.
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