Functional MRI¶
BOLD-contrast imaging for brain activity. Used for motion correction, slice timing, spatial smoothing, temporal filtering, and statistical modeling.
FSL¶
Docker image: brainlife/fsl
Motion Correction¶
| Tool | Description |
|---|---|
| Motion Correction using FLIRT (MCFLIRT) | Intra-modal motion correction for fMRI time series using rigid-body (6-DOF) transformations optimized for fMRI data. |
Slice Timing¶
| Tool | Description |
|---|---|
| FMRIB's Slice Timing Correction (SliceTimer) | Corrects for differences in slice acquisition times within each volume using sinc interpolation. |
Distortion Correction¶
| Tool | Description |
|---|---|
| FMRIB's Utility for Geometrically Unwarping EPIs (FUGUE) | Corrects geometric distortions in EPI images caused by magnetic field inhomogeneity using acquired fieldmap data. |
| Tool for Estimating and Correcting Susceptibility-Induced Distortions (TOPUP) | Estimates and corrects susceptibility-induced distortions using pairs of images with reversed phase-encode directions. |
| FSL Apply Topup Distortion Correction | Applies the susceptibility-induced off-resonance field estimated by topup to correct distortions in EPI images. |
| FSL Fieldmap Preparation | Prepares a fieldmap for use with FUGUE by converting phase difference images to radians per second. |
| FSL Phase Region Expanding Labeller for Unwrapping Discrete Estimates (PRELUDE) | Performs 3D phase unwrapping on wrapped phase images using a region-growing algorithm. |
Smoothing¶
| Tool | Description |
|---|---|
| Smallest Univalue Segment Assimilating Nucleus (SUSAN) | Edge-preserving noise reduction using nonlinear filtering that smooths within tissue boundaries while preserving edges. |
Statistical Analysis¶
| Tool | Description |
|---|---|
| FMRIB's Improved Linear Model (FILM) | Fits general linear model to fMRI time series with prewhitening using autocorrelation correction. |
| FMRIB's Local Analysis of Mixed Effects (FLAME) | Group-level mixed-effects analysis accounting for both within-subject and between-subject variance using MCMC-based B... |
| FSL Randomise Permutation Testing | Non-parametric permutation testing for statistical inference with multiple correction methods including TFCE. |
ICA/Denoising¶
| Tool | Description |
|---|---|
| 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... |
| FSL Component Regression Filter (fsl_regfilt) | Removes nuisance components from 4D fMRI data by regressing out specified columns from a design or mixing matrix. |
Pipelines¶
| Tool | Description |
|---|---|
| FMRI Expert Analysis Tool (FEAT) | Complete fMRI analysis pipeline combining preprocessing (motion correction, spatial smoothing, temporal filtering), f... |
AFNI¶
Docker image: brainlife/afni
Motion Correction¶
| Tool | Description |
|---|---|
| AFNI 3D Volume Registration (3dvolreg) | Rigid-body motion correction by registering all volumes in a 4D dataset to a base volume. |
Slice Timing¶
| Tool | Description |
|---|---|
| AFNI 3D Temporal Shift (3dTshift) | Corrects for slice timing differences by shifting each voxel time series to a common temporal reference. |
Denoising¶
| Tool | Description |
|---|---|
| AFNI 3D Despike (3dDespike) | Removes transient signal spikes from fMRI time series using an L1-norm fitting approach. |
| AFNI 3D Bandpass Filter (3dBandpass) | Applies temporal bandpass filtering to fMRI time series with optional simultaneous nuisance regression. |
Smoothing¶
| Tool | Description |
|---|---|
| AFNI 3D Adaptive Smoothing to Target FWHM | Adaptively smooths data to achieve a target smoothness level, accounting for existing smoothness. |
| AFNI 3D Merge and Smooth (3dmerge) | Combines spatial filtering and dataset merging operations, commonly used for Gaussian smoothing. |
Masking¶
| Tool | Description |
|---|---|
| AFNI 3D Automatic Mask Creation (3dAutomask) | Creates a brain mask automatically from EPI data by finding connected high-intensity voxels. |
Registration¶
| Tool | Description |
|---|---|
| AFNI align_epi_anat — EPI-to-Anatomy Alignment | Aligns EPI functional images to anatomical images with optional distortion correction using local Pearson correlation. |
Statistical Analysis¶
| Tool | Description |
|---|---|
| AFNI 3D Deconvolve (GLM Analysis) | Multiple linear regression analysis for fMRI with flexible hemodynamic response function models. |
| AFNI 3D REML Fit (Improved GLM) | GLM with ARMA(1,1) temporal autocorrelation correction using restricted maximum likelihood estimation. |
| AFNI 3D Mixed Effects Meta Analysis (3dMEMA) | Mixed effects meta-analysis for group studies that properly accounts for within and between-subject variance. |
| AFNI 3D One-Way ANOVA | Voxelwise fixed-effects one-way analysis of variance. |
| AFNI 3D Two-Way ANOVA | Voxelwise fixed-effects two-way analysis of variance with main effects and interaction. |
| AFNI 3D Three-Way ANOVA | Voxelwise fixed-effects three-way analysis of variance. |
| AFNI 3D T-Test (3dttest++) | Two-sample t-test with support for covariates, paired tests, and cluster-level inference. |
| AFNI 3D MultiVariate Modeling (3dMVM) | Multivariate modeling framework supporting ANOVA/ANCOVA designs with between and within-subject factors. |
| AFNI 3D Linear Mixed Effects (3dLME) | Linear mixed effects modeling using R lme4 package for designs with random effects. |
| AFNI 3D Linear Mixed Effects with R (3dLMEr) | Linear mixed effects with direct R formula syntax integration for flexible model specification. |
Multiple Comparisons¶
| Tool | Description |
|---|---|
| AFNI 3D Cluster Size Simulation (3dClustSim) | Simulates null distribution of cluster sizes for determining cluster-extent thresholds that control family-wise error... |
| AFNI 3D Smoothness Estimation (3dFWHMx) | Estimates spatial smoothness of data using the autocorrelation function (ACF) model. |
Connectivity¶
| Tool | Description |
|---|---|
| AFNI 3D Network Correlation Matrix (3dNetCorr) | Computes pairwise correlation matrices between ROI time series extracted from a parcellation atlas. |
| AFNI 3D Seed-Based Correlation (3dTcorr1D) | Computes voxelwise correlation between a 4D dataset and one or more 1D seed time series. |
| AFNI 3D Whole-Brain Correlation Map (3dTcorrMap) | Computes various whole-brain voxelwise correlation metrics including average correlation and global connectivity. |
| AFNI 3D Resting State Functional Connectivity (3dRSFC) | Computes resting-state frequency-domain metrics including ALFF, fALFF, mALFF, and RSFA from bandpass-filtered data. |
ROI Analysis¶
| Tool | Description |
|---|---|
| AFNI 3D ROI Statistics (3dROIstats) | Extracts statistical summary measures from data within defined ROI masks. |
| AFNI 3D Mask Average (3dmaskave) | Extracts and outputs the average time series from voxels within a mask region. |
FreeSurfer¶
Docker image: freesurfer/freesurfer
Functional Analysis¶
| Tool | Description |
|---|---|
| FreeSurfer Boundary-Based Registration (bbregister) | High-quality registration of functional EPI images to FreeSurfer anatomy using white matter boundary contrast. |
| FreeSurfer Volume to Surface Projection | Projects volumetric data (fMRI, PET, etc.) onto the cortical surface using specified sampling method. |
| FreeSurfer Surface to Volume Projection | Projects surface-based data back to volumetric space using registration and template volume. |
| FreeSurfer Surface Data Preprocessing for Group Analysis | Concatenates surface data across subjects onto a common template surface for group-level analysis. |
| FreeSurfer General Linear Model (mri_glmfit) | Fits a general linear model on surface or volume data for group-level statistical analysis. |
ANTs¶
Docker image: antsx/ants
Motion Correction¶
| Tool | Description |
|---|---|
| ANTs Motion Correction | Motion correction for time series data using ANTs registration framework with rigid or affine transformations. |
fMRIPrep¶
Docker image: nipreps/fmriprep
Pipeline¶
| 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
Pipeline¶
| 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... |
Connectome Workbench¶
Docker image: khanlab/connectome-workbench
CIFTI Operations¶
| Tool | Description |
|---|---|
| Connectome Workbench CIFTI Dense Timeseries Creation | Creates a CIFTI dense timeseries file (.dtseries.nii) combining cortical surface data with subcortical volume data in... |
| Connectome Workbench CIFTI Separate | Extracts surface or volume components from a CIFTI file into separate GIFTI metric or NIfTI volume files. |
Surface Smoothing¶
| Tool | Description |
|---|---|
| Connectome Workbench CIFTI Smoothing | Applies geodesic Gaussian smoothing to CIFTI data on cortical surfaces and Euclidean smoothing in subcortical volumes. |
| Connectome Workbench Surface Metric Smoothing | Applies geodesic Gaussian smoothing to surface metric data following the cortical surface geometry. |