Diffusion MRI¶
Diffusion-weighted imaging for white matter microstructure. Used for eddy current correction, tensor fitting, tractography, and connectivity analysis.
FSL¶
Docker image: brainlife/fsl
Preprocessing¶
| Tool | Description |
|---|---|
| FSL Eddy Current and Motion Correction (eddy) | Corrects eddy current-induced distortions and subject movement in diffusion MRI data using a Gaussian process model. |
| Tool for Estimating and Correcting Susceptibility-Induced Distortions (TOPUP) | Estimates and corrects susceptibility-induced distortions using pairs of images with reversed phase-encode directions. |
Tensor Fitting¶
| Tool | Description |
|---|---|
| FSL Diffusion Tensor Fitting (dtifit) | Fits a diffusion tensor model to each voxel of preprocessed diffusion-weighted data to generate scalar diffusion maps. |
Tractography¶
| 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... |
| Probabilistic Tractography with Crossing Fibres (probtrackx2) | Probabilistic tractography using fiber orientation distributions from bedpostx to trace white matter pathways. |
TBSS¶
| Tool | Description |
|---|---|
| TBSS Step 1: Preprocessing | Preprocesses FA images for TBSS by slightly eroding them and zeroing end slices to remove outlier voxels. |
| TBSS Step 2: Registration | Registers all FA images to a target (best subject or standard-space template) using non-linear registration. |
| TBSS Step 3: Post-Registration | Creates mean FA image and FA skeleton by projecting registered FA data onto a mean tract center. |
| TBSS Step 4: Pre-Statistics | Projects all subjects FA data onto the mean FA skeleton, ready for voxelwise cross-subject statistics. |
| TBSS Non-FA Image Projection | Projects non-FA diffusion images (MD, AD, RD, etc.) onto the mean FA skeleton using the same registration from the FA... |
MRtrix3¶
Docker image: mrtrix3/mrtrix3
Preprocessing¶
| Tool | Description |
|---|---|
| MRtrix3 DWI Denoising (MP-PCA) | Removes thermal noise from diffusion MRI data using Marchenko-Pastur PCA exploiting data redundancy across diffusion ... |
| MRtrix3 Gibbs Ringing Removal | Removes Gibbs ringing artifacts (truncation artifacts) from MRI data using a local subvoxel-shift method. |
Tensor/FOD¶
| Tool | Description |
|---|---|
| MRtrix3 Diffusion Tensor Estimation | Estimates the diffusion tensor model at each voxel from preprocessed DWI data using weighted or ordinary least squares. |
| MRtrix3 Tensor Metric Extraction | Extracts scalar metrics (FA, MD, AD, RD, eigenvalues, eigenvectors) from a fitted diffusion tensor image. |
| MRtrix3 Fiber Orientation Distribution Estimation | Estimates fiber orientation distributions (FODs) using constrained spherical deconvolution to resolve crossing fibers. |
Tractography¶
| Tool | Description |
|---|---|
| MRtrix3 Streamline Tractography Generation | Generates streamline tractograms using various algorithms (iFOD2, FACT, etc.) from FOD or tensor images. |
| MRtrix3 SIFT Tractogram Filtering | Filters tractograms to improve biological plausibility by matching streamline density to FOD lobe integrals. |
| MRtrix3 Tractogram to Connectome | Constructs a structural connectivity matrix by counting streamlines connecting pairs of regions from a parcellation. |
FreeSurfer¶
Docker image: freesurfer/freesurfer
Diffusion¶
| Tool | Description |
|---|---|
| FreeSurfer Diffusion Post-Registration Processing | Post-registration processing for diffusion MRI data as part of the TRACULA tractography pipeline. |
AMICO¶
Docker image: cookpa/amico-noddi
Microstructure Modeling¶
| Tool | Description |
|---|---|
| AMICO NODDI Fitting | Fits the NODDI (Neurite Orientation Dispersion and Density Imaging) model to multi-shell diffusion MRI data using con... |
AFNI¶
Docker image: brainlife/afni
Tensor Fitting¶
| Tool | Description |
|---|---|
| AFNI Diffusion Tensor Fitting (3dDWItoDT) | Fits a diffusion tensor model to DWI data using linear or nonlinear methods, outputting tensor components, eigenvalue... |
Uncertainty¶
| Tool | Description |
|---|---|
| AFNI DWI Uncertainty Estimation (3dDWUncert) | Estimates uncertainty of diffusion tensor parameters via jackknife or bootstrap resampling of DWI data. |
Tractography¶
| Tool | Description |
|---|---|
| AFNI Tractography (3dTrackID) | Performs deterministic, mini-probabilistic, or full probabilistic white matter tractography using diffusion tensor data. |