Awesome Neuroimaging
Exploring, organizing, and analysing brain images and recordings. 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.
- 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.