Tool Menu & Search

The left sidebar contains all available neuroimaging tools organized hierarchically: first by imaging modality, then by software library, then by functional category. The sidebar can be collapsed with the arrow button at the top to maximize canvas space. Collapse state persists across sessions.

1. Click a modality header to expand it and see the libraries within.
2. Expand a library to see individual tools grouped by category.
3. Hover over any tool to see a tooltip with its full name, function description, expected input, key parameters, and typical use case.
4. Double-click a tool in the menu to open its official documentation in a new tab.
5. Drag a tool from the menu and drop it onto the canvas to add it to your workflow.

Imaging Modalities

Tools are organized into 7 imaging modalities:

• Structural MRI — T1/T2-weighted imaging for brain anatomy. Tools for skull-stripping, tissue segmentation, cortical reconstruction, and spatial registration.
• Functional MRI — BOLD-contrast imaging for brain activity. Tools for motion correction, slice timing, spatial smoothing, temporal filtering, and statistical modeling.
• Diffusion MRI — Diffusion-weighted imaging (DWI) for white matter microstructure. Tools for eddy current correction, tensor fitting, tractography, and connectivity analysis.
• Arterial Spin Labeling (ASL) — Non-invasive perfusion imaging using magnetically labeled blood. Tools for cerebral blood flow (CBF) quantification and partial volume correction.
• PET — Positron Emission Tomography for molecular imaging. Tools for kinetic modeling, partial volume correction, and tracer-specific quantification.
• Multimodal — Cross-modality analysis pipelines. Tools that integrate structural, functional, and diffusion data for comprehensive brain mapping.
• Utilities — General-purpose neuroimaging utilities for format conversion, image math, resampling, and quality control.

Software Libraries

niBuild includes tools from 9 neuroimaging software libraries. Each library runs inside its own Docker container:

Library	Docker Image	Description
FSL	brainlife/fsl	FMRIB Software Library. Comprehensive suite for structural, functional, and diffusion analysis. Includes BET, FLIRT, FAST, FEAT, MELODIC, FDT, TBSS, and more.
AFNI	brainlife/afni	Analysis of Functional NeuroImages. Extensive tools for functional MRI analysis including motion correction, denoising, smoothing, statistical modeling, and connectivity.
FreeSurfer	freesurfer/freesurfer	Cortical surface reconstruction and parcellation. Includes recon-all for automated cortical analysis, mri_convert for format conversion, and PET processing tools.
ANTs	antsx/ants	Advanced Normalization Tools. State-of-the-art image registration (SyN), segmentation (Atropos), cortical thickness (DiReCT), and bias correction (N4).
MRtrix3	mrtrix3/mrtrix3	Diffusion MRI analysis toolkit. Specializes in constrained spherical deconvolution (CSD), fiber orientation distribution (FOD) estimation, and anatomically-constrained tractography (ACT).
Connectome Workbench	khanlab/connectome-workbench	HCP Connectome tools for surface-based analysis. CIFTI file operations and surface data smoothing for cortical analysis.
fMRIPrep	nipreps/fmriprep	Robust, automated fMRI preprocessing pipeline. Produces analysis-ready BOLD data with comprehensive quality reports.
MRIQC	nipreps/mriqc	MRI Quality Control. Extracts image quality metrics (SNR, CNR, motion parameters) and generates visual quality reports.
AMICO	cookpa/amico-noddi	Accelerated Microstructure Imaging via Convex Optimization. Fits biophysical models (NODDI) to diffusion MRI data for neurite density and orientation dispersion.

Library Coverage by Modality

Library	Structural	Functional	Diffusion	ASL	PET	Multimodal	Utilities
FSL	✓	✓	✓	✓			✓
AFNI	✓	✓					✓
FreeSurfer	✓	✓	✓		✓		✓
ANTs	✓	✓				✓	✓
MRtrix3			✓
Workbench	✓	✓
fMRIPrep		✓
MRIQC		✓
AMICO			✓

Search

• Type in the search bar to filter tools by name, function description, or modality.
• Use modality prefix syntax for targeted filtering:
  • Structural MRI/ — shows all structural MRI tools
  • MRI/bet — searches for "bet" within all MRI modalities
  • Diffusion/ — shows all diffusion tools
• Custom workflows are also searchable by name or by the tools they contain.

I/O Nodes

The "I/O" section at the top of the menu contains special nodes that define pipeline entry and exit points:

• Workflow Input — defines an input file or value that the user supplies when running the pipeline.
• Workflow Output — collects specific results as final pipeline outputs. Connect it to upstream nodes, then double-click to open the Output Configuration modal where you can select exactly which outputs to include.
• BIDS Dataset — imports files from a BIDS-compliant dataset directory (see BIDS Integration).