Pipelines¶
Complete multi-step analysis pipelines that chain several operations internally. Each tool orchestrates preprocessing, registration, segmentation, or analysis stages as a single command.
FSL¶
Docker image: brainlife/fsl
Structural¶
| 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... |
| FMRIB's Integrated Registration and Segmentation Tool (FIRST) | Multi-step pipeline for subcortical structure segmentation. Internally chains registration, boundary correction, and ... |
Functional¶
| Tool | Description |
|---|---|
| FMRI Expert Analysis Tool (FEAT) | Complete fMRI analysis pipeline combining preprocessing (motion correction, spatial smoothing, temporal filtering), f... |
| Multivariate Exploratory Linear Optimized Decomposition into Independent Components (MELODIC) | Multi-step ICA pipeline that decomposes fMRI data into spatially independent components. Internally chains brain mask... |
| FSL Dual Regression | Multi-step pipeline that projects group-level ICA spatial maps back to individual subjects. Internally chains spatial... |
Diffusion¶
| Tool | Description |
|---|---|
| Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques (BEDPOSTX) | Multi-step pipeline for Bayesian estimation of fiber orientation distributions. Internally runs multi-fiber MCMC samp... |
ASL¶
| Tool | Description |
|---|---|
| Oxford ASL Processing Pipeline | Multi-step pipeline for ASL MRI quantification. Internally chains motion correction, registration, BASIL kinetic mode... |
ANTs¶
Docker image: antsx/ants
Structural¶
| Tool | Description |
|---|---|
| ANTs Cortical Thickness Pipeline | Complete automated pipeline for cortical thickness estimation using DiReCT, including brain extraction, segmentation,... |
| ANTs Combined Atropos with N4 Bias Correction | Iteratively combines N4 bias field correction with Atropos segmentation for improved results on biased images. |
FreeSurfer¶
Docker image: freesurfer/freesurfer
Surface Reconstruction¶
| Tool | Description |
|---|---|
| FreeSurfer Complete Cortical Reconstruction Pipeline | Fully automated pipeline for cortical surface reconstruction and parcellation, including skull stripping, segmentatio... |
fMRIPrep¶
Docker image: nipreps/fmriprep
fMRI Preprocessing¶
| Tool | Description |
|---|---|
| fMRIPrep: Robust fMRI Preprocessing Pipeline | Automated, robust preprocessing pipeline for task-based and resting-state fMRI, combining tools from FSL, FreeSurfer,... |
MRIQC¶
Docker image: nipreps/mriqc
Quality Control¶
| Tool | Description |
|---|---|
| MRIQC: MRI Quality Control Pipeline | Multi-step quality control pipeline. Internally chains brain extraction, spatial normalization, and computation of do... |
ICA-AROMA¶
Docker image: rtrhd/ica-aroma
Denoising¶
| Tool | Description |
|---|---|
| ICA-based Automatic Removal of Motion Artifacts (ICA-AROMA) | Multi-step denoising pipeline for fMRI motion artifact removal. Internally chains MELODIC ICA decomposition, motion a... |