diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml new file mode 100644 index 0000000..c73321a --- /dev/null +++ b/.github/workflows/main.yaml @@ -0,0 +1,22 @@ +name: CI +on: + - push + - pull_request +jobs: + test: + name: Node.js 20 + runs-on: ubuntu-latest + strategy: + fail-fast: false + steps: + - uses: actions/checkout@v4 + with: + submodules: true + fetch-depth: 0 + - uses: actions/setup-node@v4 + with: + node-version: 20 + - run: npm install + - run: npm test + env: + github_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..504afef --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +node_modules/ +package-lock.json diff --git a/license b/license new file mode 100644 index 0000000..9ab28a0 --- /dev/null +++ b/license @@ -0,0 +1,40 @@ +CC0 1.0 Universal + +Statement of Purpose + +The laws of most jurisdictions throughout the world automatically confer exclusive Copyright and Related Rights (defined below) upon the creator and subsequent owner(s) (each and all, an "owner") of an original work of authorship and/or a database (each, a "Work"). + +Certain owners wish to permanently relinquish those rights to a Work for the purpose of contributing to a commons of creative, cultural and scientific works ("Commons") that the public can reliably and without fear of later claims of infringement build upon, modify, incorporate in other works, reuse and redistribute as freely as possible in any form whatsoever and for any purposes, including without limitation commercial purposes. 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MR focused. - ## Contents - [Viewers](#viewers) -- [Acquisition](#acquistion) -- [Quality Assurance and Checking](#mri-pipelines) +- [Acquisition](#acquisition) + - [MR](#mr) +- [Quality Assurance and Checking](#quality-assurance-and-checking) - [Pipelines](#pipelines) + - [Suites](#suites) + - [BOLD](#bold) + - [DSI](#dsi) + - [Structural](#structural) - [Raw Data](#raw-data) +- [Provenance and Automation](#provenance-and-automation) +- [Imaging Tools](#imaging-tools) + - [Warping](#warping) + - [Manipulation](#manipulation) + - [Modeling](#modeling) - [Libraries](#libraries) - [Resources](#resources) + - [Blogs, Books, and Docs](#blogs-books-and-docs) + - [Boards And Chats](#boards-and-chats) + - [Datasets Repositories](#datasets-repositories) ## Viewers - - [AFNI](https://afni.nimh.nih.gov/) - - freeview ([Freesurfer](https://freesurfer.net/)) - - fsleyes ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)) - - [mricron](https://www.nitrc.org/projects/mricron) - - [dsistudio](https://dsi-studio.labsolver.org/) - - [osirix](https://www.osirix-viewer.com/) +- [AFNI](https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/afniandafni/gui_guide/main_toc.html) - Volumetric viewer from the AFNI suit. GUI's aesthetic defined by the '90s era Motif toolkit. +- [freeview](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewIntroduction) - Surface and volumetric image viewer in Freesurfer suit. Uses the QT toolkit. +- [fsleyes](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLeyes) - Volumetric viewer from FSL. +- [mricron](https://www.nitrc.org/projects/mricron) - Volumetric viewer that works on windows. +- [dsistudio](https://dsi-studio.labsolver.org/doc/gui_t1.html) - DSI viewer from the dsi-studio suit of tools. +- [osirix](https://www.osirix-viewer.com/) - DICOM database organizer and viewer. ## Acquisition ### MR #### Organization - - [reproIn](https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html) - naming exam card sequences - - [BIDS](https://bids-specification.readthedocs.io/en/stable/) - Brain Imaging Data Structure - directory hierarchy and file naming specification +- [reproIn](https://dbic-handbook.readthedocs.io/en/latest/mri/reproin.html) - Naming exam card sequences. +- [BIDS](https://bids-specification.readthedocs.io/en/stable/) - Brain Imaging Data Structure - directory hierarchy and file naming specification. #### Management -- PACS - Picture Archiving and Communication System -- [XNAT](https://www.xnat.org/) - - [DAX](https://github.com/VUIIS/dax) Distributed Automation for XNAT: use containerization w/YAML defined input/output -- [LORIS](https://mcin.ca/technology/loris/) & [cbrain](https://mcin.ca/technology/cbrain/) -- [Flywheel](flywheel.io) - $$$ -- [QMENTA](https://qmenta.com) - $$$ +- PACS - Picture Archiving and Communication System. +- [XNAT](https://www.xnat.org/) - An extensible open-source imaging informatics software platform dedicated to imaging-based research. + - [DAX](https://github.com/VUIIS/dax) - Distributed Automation for XNAT: use containerization w/YAML defined input/output. +- [LORIS](https://mcin.ca/technology/loris/) - LORIS (Longitudinal Online Research and Imaging System) is web-based data and project management software for neuroimaging research studies. +- [cbrain](https://mcin.ca/technology/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](https://flywheel.io) - A cloud-based imaging research data platform for data capture, curating, automation, and machine learning. +- 💲[QMENTA](https://qmenta.com) - The all in one imaging platform for your clinical trial. #### Motion -- [FIRMM](https://firmm.readthedocs.io) -- [`Dimon`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/Dimon.html) +- [FIRMM](https://firmm.readthedocs.io) - Real-time motion monitoring for fMRI, diffusion, and navigated T1/T2 image acquisition. +- [`Dimon`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/Dimon.html) - Monitor real-time acquisition of DICOM image files with AFNI. ## Quality Assurance and Checking QA and QC of scanner images. -- [MRIQC](https://mriqc.readthedocs.io/) -- [mrQA](https://github.com/Open-Minds-Lab/mrQA) -- [bids-validator](https://github.com/bids-standard/bids-validator/) +- [MRIQC](https://mriqc.readthedocs.io/) - Extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data. +- [mrQA](https://github.com/Open-Minds-Lab/mrQA) - Tools for quality assurance in medical imaging datasets, including protocol compliance. +- [bids-validator](https://github.com/bids-standard/bids-validator/) - Validator for the Brain Imaging Data Structure. ## Pipelines @@ -55,116 +68,128 @@ Preprocessing workflows. ### Suites Software packages for multiple modalities, often offering a graphical user interface. - - [AFNI](https://afni.nimh.nih.gov/) - - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) - - [SPM](https://www.fil.ion.ucl.ac.uk/spm/) - - [Qu|Nex](https://qunex.yale.edu/) + +- [AFNI](https://afni.nimh.nih.gov/) - 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](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) - A comprehensive library of analysis tools for FMRI, MRI and diffusion brain imaging data. +- [SPM](https://www.fil.ion.ucl.ac.uk/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](https://qunex.yale.edu/) - 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](fmriprep.org/) -- [`afni_proc.py`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html) -- [HALFpipe](https://github.com/HALFpipe/HALFpipe) -- [XCP](https://xcpengine.readthedocs.io/) -- [clpipe](https://clpipe.readthedocs.io/en/latest/) -- [fmri_processing_scripts](https://github.com/LabNeuroCogDevel/fmri_processing_scripts) +- [fmriprep](https://fmriprep.org/) - Accessible preprocessing pipeline robust to variations in scan acquisition protocols with comprehensive error and output reporting. Input is BIDS dataset. +- [`afni_proc.py`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html) - Best practice pipelines with pre-configured blocks using AFNI. +- [HALFpipe](https://github.com/HALFpipe/HALFpipe) - User-friendly software that facilitates reproducible analysis of fMRI data. +- [XCP-D](https://xcp-d.readthedocs.io/en/latest/) - Post-processing and noise regression pipeline picks up right where fMRIprep ends. +- [clpipe](https://clpipe.readthedocs.io/en/latest/) - 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](https://github.com/LabNeuroCogDevel/fmri_processing_scripts) - Legacy pipeline for maximal preprocessing. ### DSI -- [dsi-studio](https://dsi-studio.labsolver.org/) -- [qsiprep](https://qsiprep.readthedocs.io/) +- [dsi-studio](https://dsi-studio.labsolver.org/) - A tractography software tool that maps brain connections and correlates findings with neuropsychological disorders. +- [qsiprep](https://qsiprep.readthedocs.io/) - Configures pipelines for processing diffusion-weighted MRI (dMRI) data. ### Structural -- [Freesurfer](https://freesurfer.net/) -- [CIVET](https://mcin.ca/technology/civet/) +- [Freesurfer](https://freesurfer.net/) - An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images. +- [CIVET](https://mcin.ca/technology/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](https://github.com/rordenlab/dcm2niix) -- [heudiconv](https://github.com/nipy/heudiconv/) -- [`dicom_hinfo`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/dicom_hinfo.html) -- [`dcmdirtab`, `dcmtab_bids`](https://lncd.github.io/lncdtools/BIDS/) (from [lncdtools](https://github.com/lncd/lncdtools/)) -- mapVBVD +- [dcm2niix](https://github.com/rordenlab/dcm2niix) - DICOM to NIfTI converter. +- [heudiconv](https://github.com/nipy/heudiconv/) - A flexible DICOM converter for organizing brain imaging data into structured directory layouts. +- [`dicom_hinfo`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/dicom_hinfo.html) - Prints selected information from the DICOM file. + +- [`dcmdirtab`, `dcmtab_bids`](https://lncd.github.io/lncdtools/BIDS/) - CLI focused, regular expression based, and iteration friendly BIDS conversion pipeline from [lncdtools](https://github.com/lncd/lncdtools/). +- [pymapVBVD](https://git.fmrib.ox.ac.uk/wclarke/pymapvbvd) - Reads Siemens .dat 'twix' raw data files. Python port of Philipp Ehses' Matlab tool mapVBVD. -## Provenance and automation +## Provenance and Automation -- [make](https://www.frontiersin.org/articles/10.3389/fninf.2016.00002/full) -- [datalad](https://handbook.datalad.org/) - esp `datalad run --input=... --output=...` -- `niinote` ([lncdtools](https://github.com/lncd/lncdtools/)) -- `3dNotes` ([AFNI](https://afni.nimh.nih.gov/)) +- [make](https://www.frontiersin.org/articles/10.3389/fninf.2016.00002/full) - follow script recipes defined in `Makefile`. +- [datalad](https://github.com/datalad/datalad) - Keep code, data, containers under control with git and git-annex. Esp `datalad run --input=... --output=...`. +- [`3dNotes`](https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dNotes.html) - A program to add, delete and show notes for AFNI datasets. + +- [`niinote`](https://github.com/lncd/lncdtools/blob/master/niinote) - Add AFNI nifti XML history to header to run and record any command. Part of [lncdtools](https://github.com/lncd/lncdtools/). -## Imaging tools +## Imaging Tools +Software to read, write, and manipulate volumetric and/or surface data. ### Warping -spatial normalization +Spatial normalization -- [ANTs](http://stnava.github.io/ANTs/) -- 3dNwarpApply - NB. OpenMP parallelized! ([AFNI](https://afni.nimh.nih.gov/)) -- flirt, fnirt ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)) +- [ANTs](http://stnava.github.io/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](https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dQwarp.html) - OpenMP parallelized [AFNI](https://afni.nimh.nih.gov/) tool to compute a nonlinearly warped version of source dataset to match a base dataset. + +- [flirt, fnirt](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT/UserGuide) - Warping software provided by [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) tools. #### Templates -- [templateflow](https://www.templateflow.org/) -- [MNI152](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) +- [templateflow](https://www.templateflow.org/) - A modular, version-controlled resource that allows researchers to use templates "off-the-shelf" and share new ones. +- [MNI152](https://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009) - Unbiased standard magnetic resonance imaging template brain volume for normal population. ### Manipulation +Tools for doing math on matrix values -- 3dcalc ([AFNI](https://afni.nimh.nih.gov/)) -- fslmaths ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)) -- fscalc ([Freesurfer](https://freesurfer.net/)) -- also see [#Libraries](#libraries) for development interfaces to be used within programming language +- [3dcalc](https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dcalc.html) - Voxel-by-voxel arithmetic on 1D to 4D datasets. From AFNI. +- [fslmaths](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils#:~:text=a%20combined%20image.-,fslmaths,--%20simple%20but%20powerful) - Simple but powerful program to allow mathematical manipulation of images. From FSL. +- [fscalc](https://www.freesurfer.net/pub/dist/freesurfer/dev_binaries/centos6_x86_64/fscalc.fsl) - Freesurfer wrapper of fslmaths. + ### Modeling #### HRF -- 3dDeconvolve ([AFNI](https://afni.nimh.nih.gov/)) -- FEAT ([FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)) + + +- [3dDeconvolve](https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dDeconvolve.html) - [AFNI](https://afni.nimh.nih.gov/) - 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](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT) - GUI guided analysis of simple experiment based on general linear modeling. Part of [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki). #### MRSI -- [lcmodel](https://github.com/schorschinho/LCModel) + +- [lcmodel](https://github.com/schorschinho/LCModel) - Implements linear-combination modeling of magnetic resonance spectroscopy data. +- [FSL-MRS](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/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](https://github.com/schorschinho/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](https://lncd.github.io/lncdtools/tat2/) + +- [tat2](https://lncd.github.io/lncdtools/tat2/) - Time-averaged T2* wrapper script using AFNI binaries from [lncdtools](https://github.com/lncd/lncdtools/). ## Libraries ### Python -- [nipy](https://nipy.org/) - - nibabel - - nipype - - nilearn +- [nipy](https://nipy.org/) - Includes `nibabel`, `nipype`, and `nilearn`. ### R -- [oro.nifti](https://github.com/bjw34032/oro.nifti) +- [oro.nifti](https://github.com/bjw34032/oro.nifti) - Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats. ### MATLAB -- [SPM](https://www.fil.ion.ucl.ac.uk/spm/) -- [`imtool3D_td`](https://github.com/tanguyduval/imtool3D_td) + +- [SPM](https://www.fil.ion.ucl.ac.uk/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`](https://github.com/tanguyduval/imtool3D_td) - 3D Image Viewer with ROI tools for Matlab (NIFTI viewer, Manual segmentation). ## Resources ### Blogs, Books, and Docs -- [andy's brain blog](andysbrainblog.com/) +- [andy's brain blog](https://andysbrainblog.com/) - [datalad handbook](https://handbook.datalad.org/) - [Hitchhacker's guide to the brain/](https://learn-neuroimaging.github.io/hitchhackers_guide_brain/) - [Online Neuroimaging Resources](https://github.com/Remi-Gau/online_neuroimaging_resources) ### Boards And Chats -- [neurostars](https://neurostars.org/) -- [afni discuss](https://discuss.afni.nimh.nih.gov) -- [brainhack](https://mattermost.brainhack.org/) +- [neurostars](https://neurostars.org/) - General nueroimaging `dicuss` form. `fmriprep` suggested Q&A site. +- [afni discuss](https://discuss.afni.nimh.nih.gov) - AFNI's `discuss` instance. +- [brainhack](https://mattermost.brainhack.org/) - A mattermoust community of neuroimagers. ### Datasets Repositories