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Neuroimaging

repo: NPACore/awesome-neuroimaging
category: Health and Social Science

Awesome Neuroimaging Awesome

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](https://www.gehealthcare.com/products/healthcare-it/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.

Imaging Tools

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](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 - 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.

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