Awesome Neuroimaging

Exploring, organizing, and analysing neuro-images. MR focused.

Contents

• Viewers
• Acquisition
  • MR
• Quality Assurance and Checking
• Pipelines
  • Suites
  • BOLD
  • DSI
  • Structural
• Raw Data
• Provenance and Automation
• Imaging Tools
  • Skullstripping
  • Warping
  • Manipulation
  • Modeling
• Libraries
• Resources
  • Blogs, Books, and Docs
  • Boards And Chats
  • Datasets Repositories

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.

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.
• 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.
• 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.

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.
• dicom_hinfo - 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.

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

• 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.

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

Misc

• hurst

• tat2 - Time-averaged T2* wrapper script using AFNI binaries from lncdtools.

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
• datalad handbook
• Hitchhacker's guide to the brain/
• Online Neuroimaging Resources
• U of A: Neuroimaging Core Documentation

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
• NDA
• NITRC

Big datasets

• ABCD
• UK Biobank
• NCANDA
• PNC
• ENIGMA

Contributing

Contributions welcome! Read the contribution guidelines first.