Structural MRI¶

T1/T2-weighted imaging for brain anatomy. Used for skull-stripping, tissue segmentation, cortical reconstruction, and spatial registration.

FSL¶

Docker image: brainlife/fsl

Tool	Description
Brain Extraction Tool (BET)	Removes non-brain tissue from MRI images using a deformable surface model that iteratively fits to the brain boundary.

Tool	Description
FMRIB's Automated Segmentation Tool (FAST)	Segments brain images into gray matter, white matter, and CSF using a hidden Markov random field model with integrate...
FMRIB's Integrated Registration and Segmentation Tool (FIRST)	Multi-step pipeline for subcortical structure segmentation. Internally chains registration, boundary correction, and ...

Tool	Description
FMRIB's Linear Image Registration Tool (FLIRT)	Linear (affine) registration between images using optimized cost functions with 6, 7, 9, or 12 degrees of freedom.
FMRIB's Non-linear Image Registration Tool (FNIRT)	Non-linear registration using B-spline deformations for precise anatomical alignment to a template.

Tool	Description
FSL Anatomical Processing Pipeline	Comprehensive automated pipeline for structural T1 processing including reorientation, cropping, bias correction, reg...
Structural Image Evaluation using Normalisation of Atrophy (SIENA)	Multi-step pipeline that estimates percentage brain volume change between two timepoints. Internally chains BET brain...
SIENA Cross-Sectional (SIENAX)	Multi-step pipeline for cross-sectional brain volume estimation. Internally chains BET brain extraction, atlas regist...

Tool	Description
Brain Intensity AbNormality Classification Algorithm (BIANCA)	Automated white matter hyperintensity (WMH) segmentation using supervised machine learning (k-nearest neighbor) train...

Docker image: antsx/ants

Tool	Description
ANTs Template-Based Brain Extraction	High-quality brain extraction using registration to a brain template and tissue priors for robust skull stripping.

Tool	Description
ANTs Atropos Tissue Segmentation	Probabilistic tissue segmentation using expectation-maximization algorithm with Markov random field spatial prior.
ANTs Combined Atropos with N4 Bias Correction	Iteratively combines N4 bias field correction with Atropos segmentation for improved results on biased images.

Tool	Description
ANTs Multi-Stage Image Registration	State-of-the-art image registration supporting multiple stages (rigid, affine, SyN) with configurable metrics and con...
ANTs SyN Registration with Defaults	Symmetric normalization registration with sensible default parameters for common registration tasks.
ANTs Quick SyN Registration	Fast SyN registration with reduced iterations and coarser sampling for rapid approximate registration.

Tool	Description
ANTs Cortical Thickness Pipeline	Complete automated pipeline for cortical thickness estimation using DiReCT, including brain extraction, segmentation,...
ANTs DiReCT Cortical Thickness (KellyKapowski)	Estimates cortical thickness using the DiReCT algorithm from segmentation data.

Docker image: freesurfer/freesurfer

Tool	Description
FreeSurfer Complete Cortical Reconstruction Pipeline	Fully automated pipeline for cortical surface reconstruction and parcellation, including skull stripping, segmentatio...
FreeSurfer MRI Format Conversion (mri_convert)	Converts between neuroimaging file formats (DICOM, NIfTI, MGH/MGZ, ANALYZE, etc.) with optional resampling and confor...
FreeSurfer MRI Watershed Skull Stripping	Brain extraction using a hybrid watershed/surface deformation algorithm to find the brain-skull boundary.
FreeSurfer MRI Intensity Normalization	Normalizes T1 image intensities so that white matter has a target intensity value (default 110).
FreeSurfer MRI White Matter Segmentation	Segments white matter from normalized T1 image using intensity thresholding and morphological operations.
FreeSurfer Surface Inflation	Inflates folded cortical surface to a smooth shape while minimizing metric distortion for visualization.
FreeSurfer Surface to Sphere Mapping	Maps the inflated cortical surface to a sphere for inter-subject spherical registration.

Tool	Description
FreeSurfer Cortical Parcellation to Volume	Combines surface-based cortical parcellation (aparc) with volumetric subcortical segmentation (aseg) into a single vo...
FreeSurfer Annotation to Individual Labels	Extracts individual region labels from a surface annotation file into separate label files.
FreeSurfer Cortical Atlas Labeling	Applies a cortical parcellation atlas to an individual subject using trained classifier on spherical surface.
FreeSurfer Label to Volume Conversion	Converts surface-based labels to volumetric ROIs using a registration matrix.

Tool	Description
FreeSurfer Surface Anatomical Statistics	Computes surface-based morphometric measures (thickness, area, volume, curvature) for each region in a parcellation.
FreeSurfer Segmentation Statistics	Computes volume and intensity statistics for each region in a segmentation volume.
FreeSurfer Cortical Stats to Group Table	Collects cortical parcellation statistics across multiple subjects into a single table for group analysis.
FreeSurfer Subcortical Stats to Group Table	Collects subcortical segmentation statistics across multiple subjects into a single table.

Docker image: brainlife/afni

Tool	Description
AFNI 3D Skull Strip	Removes non-brain tissue using a modified spherical surface expansion algorithm adapted from BET.
AFNI Skull Strip and Nonlinear Warp (@SSwarper)	Combined skull stripping and non-linear warping to template in a single optimized pipeline.

Tool	Description
AFNI 3D Intensity Uniformization (3dUnifize)	Corrects intensity inhomogeneity (bias field) to produce uniform white matter intensity.

Tool	Description
AFNI 3D Affine Registration (3dAllineate)	Linear (affine) registration with multiple cost functions and optimization methods.
AFNI 3D Nonlinear Warp (3dQwarp)	Non-linear registration using cubic polynomial basis functions for precise anatomical alignment.
AFNI Automated Talairach Transformation (@auto_tlrc)	Automated Talairach transformation using affine registration to a template atlas.

Docker image: khanlab/connectome-workbench

Tool	Description
Connectome Workbench Surface Registration Transform	Applies MSM or FreeSurfer spherical registration by projecting coordinates through registered sphere to target space.