28 projects
niwrap-workbench
Connectome Workbench is an open-source visualization and discovery tool developed for the Human Connectome Project (HCP) at Washington University in St. Louis. It includes wb_view, a GUI-based visualization platform for exploring brain imaging data on cortical surfaces and volumes, and wb_command, a command-line program for performing algorithmic tasks using volume, surface, and grayordinate (CIFTI) data. wb_command is essential for running HCP minimal processing pipelines.
niwrap-niftyreg
NiftyReg is an open-source medical image registration toolkit that provides tools for rigid, affine, and non-linear registration of medical images. It implements a block-matching approach (reg_aladin) for global registration and a fast free-form deformation algorithm based on cubic B-splines (reg_f3d) for non-linear registration, with both CPU and GPU implementations. NiftyReg was developed at the Centre for Medical Image Computing (CMIC) at University College London.
niwrap-mrtrix3tissue
MRtrix3Tissue is a fork of MRtrix3 that adds capabilities for 3-Tissue Constrained Spherical Deconvolution (CSD) modelling and analysis. It provides Single-Shell 3-Tissue CSD (SS3T-CSD), enabling multi-tissue CSD analysis from single-shell diffusion MRI data without requiring multi-shell acquisitions.
niwrap-mrtrix
MRtrix3 is a fast, flexible, and open software framework for medical image processing and visualisation, with a particular focus on diffusion MRI analysis. It provides tools for constrained spherical deconvolution, anatomically-constrained tractography, fixel-based analysis, and next-generation group-level analyses. It is freely available under the Mozilla Public License v2.0.
niwrap-greedy
Greedy is a tool for fast deformable registration of 2D and 3D medical images. Developed at the Penn Image Computing and Science Lab (PICSL), it was designed for really fast CPU-based deformable image registration in applications where many images must be registered in parallel, such as multi-atlas segmentation. Greedy borrows concepts from Symmetric Normalization (SyN) in ANTs but uses a non-symmetric approach and highly optimized metric computation code for additional speed.
niwrap-fsl
FSL (FMRIB Software Library) is a comprehensive library of analysis tools for FMRI, MRI, and diffusion brain imaging data, developed by the FMRIB Analysis Group at the University of Oxford. It includes tools for brain extraction, image registration, structural and functional analysis, tractography, ICA-based analysis, and statistical inference. Most tools can be run both from the command line and as GUIs.
niwrap-freesurfer
FreeSurfer is a software package for the analysis and visualization of neuroimaging data from cross-sectional and longitudinal studies, developed by the Laboratory for Computational Neuroimaging at the Martinos Center for Biomedical Imaging.
niwrap-fastsurfer
FastSurfer is a fast and accurate deep-learning-based neuroimaging pipeline that provides a full FreeSurfer alternative for volumetric analysis (via FastSurferVINN) and surface-based thickness analysis (via recon-surf). It can segment a whole brain MRI scan in under one minute on a GPU and produces FreeSurfer-compatible outputs, making it a drop-in replacement for FreeSurfer's recon-all pipeline.
niwrap-dcm2niix
dcm2niix converts neuroimaging data from the DICOM format to NIfTI format. It handles all major MRI vendors (Siemens, GE, Philips), supports lossy and lossless compression, and can generate Brain Imaging Data Structure (BIDS) sidecar JSON files. dcm2niix is the successor to dcm2nii and is designed for fast, reliable batch conversion of DICOM images.
niwrap-c3d
Convert3D (c3d) is a command-line tool for medical image processing that offers complementary features to ITK-SNAP. It provides standard filters, resampling commands, and tools specialized for multilabel and multicomponent images. Through the use of reverse polish notation on the command line, c3d allows many image processing tasks to be combined in small command-line mini-programs without saving intermediate image files.
niwrap-ants
Advanced Normalization Tools (ANTs) computes high-dimensional mappings to capture the statistics of brain structure and function. It is a state-of-the-art medical image registration and segmentation toolkit that allows one to organize, visualize, and statistically explore large biomedical image sets. ANTs integrates imaging modalities in space and time and works across species or organ systems with minimal customization.
niwrap-afni
AFNI (Analysis of Functional NeuroImages) is a suite of programs for the analysis and visualization of multiple MRI modalities: anatomical, functional MRI (FMRI), and diffusion weighted (DW) data. Developed and maintained at the National Institute of Mental Health (NIMH), AFNI provides a comprehensive environment for processing, analyzing, and visualizing neuroimaging data, including real-time FMRI capabilities. It is freely available as open source software for research purposes.
niwrap
Neuroimaging wrappers.
styxsingularity
Singularity/Apptainer integration for Styx compiled wrappers.
styxpodman
Podman integration for Styx compiled wrappers.
styxcache
Content-addressed caching middleware for Styx
styxcontainer-common
Shared base classes for Styx container runners.
styxdocker
Docker integration for Styx compiled wrappers.
styxgraph
Execution graph middleware for Styx
styxdefs
Styx definitions and minimal runtime
actfast
None
argdump
Serialize and deserialize argparse parsers
cloai
A generic interface for AI models.
styxcompiler
Boutiques code generator
ba-tsconcat
BIDS App and Python library for concatenating MRI time series.
mrirage
MRI visualization
textknnassifier
TextKNNClassifier is a k-nearest neighbors classifier for text data. It uses a compression algorithm to compute the distance between texts and predicts the label of a test entry based on the labels of the k-nearest neighbors in the training data.
flowdump
NiPype-1 workflow serializer.
