# 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.

- 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

- 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` - Fast, efficient, and physiologically-informed tool to parameterize neural power spectra.

#### Misc

- 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`.

### 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