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awesome-neuroimaging

Exploring, organizing, and analysing neuroimages (MR focus)
https://github.com/NPACore/awesome-neuroimaging

Last synced: about 20 hours ago
JSON representation

  • Viewers

    • mricron - Volumetric viewer that works on windows.
    • dsistudio - DSI viewer from the dsi-studio suit of tools.
    • osirix - DICOM database organizer and viewer.
    • 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.

  • 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](https://www.siemens-healthineers.com/en-us/digital-health-solutions/syngo-carbon), [Phillips Vue PACS](https://www.documents.philips.com/assets/20240227/5a788a79bbdd4e1986f1b12300b0e534.pdf), [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.
      • 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

    • MR

      • mrQA - Tools for quality assurance in medical imaging datasets, including protocol compliance.

  • 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.
      • 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.
      • MINC - - more of a format than suit? -->

    • BOLD

      • fmri_processing_scripts - Legacy pipeline for maximal preprocessing.
      • `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.

    • DSI

      • dsi-studio - A tractography software tool that maps brain connections and correlates findings with neuropsychological disorders.

    • 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

    • Structural

      • dcm2niix - DICOM to NIfTI converter.
      • `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](https://github.com/lncd/lncdtools/).
      • pymapVBVD - Reads Siemens .dat 'twix' raw data files. Python port of Philipp Ehses' Matlab tool mapVBVD.

  • Provenance and Automation

    • Structural

      • 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](https://github.com/lncd/lncdtools/).

  • Imaging Tools

    • Skullstripping

      • optibet - Shell script to combine afni and fsl tools for more robust skull stripping in patient populations.
      • `3dSkullStrip` - [AFNI](https://afni.nimh.nih.gov/)'s skull stripping utility with many parameters.
      • `antsBrainExtraction.sh` - [ANTs](http://stnava.github.io/ANTs/) version.
      • `mri-watershed` - Part of the [Freesurfer](https://freesurfer.net/) pipeline.
      • ROBEX - Robust Brain Extraction without parameter tweaking.
Programming Languages
Python 4 C++ 1 Shell 1
Categories
Pipelines 12 Acquisition 12 Viewers 5 Imaging Tools 5 Raw Data 4 Provenance and Automation 4 Quality Assurance and Checking 1
Sub Categories
MR 13 Structural 10 Skullstripping 5 BOLD 5 Suites 4 DSI 1
Keywords
neuroimaging 3 python 2 fmri 2 mri 2 mri-images 2 neuroscience 2 dcm2niix 1 dcm 1 bids-format 1 fmri-preprocessing 1 quality-control 1 quality-assurance 1 qa 1 niqc 1 mri-brain 1 mr-image 1 ismrm 1 brain 1 xnat 1 dax 1 reproducibility 1 pipeline 1 meta-analysis 1 bids 1 usable 1 git-annex 1 dataset 1 data-storage 1 closember 1 research 1 nitrc 1 nii 1 nifti-format 1 nifti 1 mricrogl 1 jpeg-image 1 jpeg 1 gz 1 dicom-images 1 dicom 1