DSI Studio: A Beginner’s Guide to Diffusion MRI Tractography—
Introduction
Diffusion MRI (dMRI) is a noninvasive imaging technique that maps the diffusion of water molecules in biological tissue. In the brain, water diffusion is constrained by white matter fibers, so dMRI provides an indirect measure of neural pathways. Tractography uses diffusion MRI data to reconstruct probable trajectories of these fiber bundles, producing 3D models called streamlines that approximate white matter tracts.
DSI Studio is a widely used, user-friendly software package for diffusion MRI processing, reconstruction, and tractography. It supports multiple reconstruction methods (including GQI and Q-ball), offers both deterministic and probabilistic tracking, provides tools for connectome analysis and fiber quantification, and includes a responsive graphical interface and command-line options. This guide introduces the basic concepts, data preparation steps, common workflows in DSI Studio, and practical tips for beginners.
Key concepts
- Diffusion weighting (b-values): Measures sensitivity to diffusion. Higher b-values emphasize slower diffusion and microstructural detail but require higher SNR.
- Gradient directions: Number and distribution of gradient directions affect angular resolution. More directions improve orientation estimation.
- Diffusion models: Algorithms that estimate fiber orientation distribution functions (ODFs) or orientation density from raw dMRI data. Examples: Diffusion Tensor Imaging (DTI), Q-ball imaging, Generalized Q-sampling Imaging (GQI).
- Orientation Distribution Function (ODF): A function describing the likelihood of water diffusion in each direction; used as a basis for tractography.
- Tractography: Streamline propagation using local orientation information. Deterministic tractography follows the principal direction; probabilistic tractography samples from orientation uncertainty.
- ROIs (Regions of Interest): Masks used to include or exclude streamlines for focused tract reconstruction.
- Connectome: Graph representation of brain connectivity; nodes = brain regions, edges = tractography-derived connections (often weighted by fiber count, density, or microstructural metrics).
Installing and launching DSI Studio
DSI Studio is cross-platform (Windows, macOS, Linux). Download the latest release from the official site and extract the archive. No complex installation is required—run the executable.
Minimum steps:
- Download DSI Studio for your OS.
- Extract/unpack the files.
- Run the DSI Studio executable (dsistudio or DSIStudio.exe).
Command-line usage is available for batch processing: dsistudio –command_line_mode … (see built-in help for specifics).
Preparing your diffusion data
DSI Studio accepts multiple input formats (e.g., NIfTI, DICOM, .src/.fib formats). Typical pipeline:
- Convert raw scanner DICOMs to NIfTI and extract b-values and b-vectors (bvec/bval). Tools like dcm2niix are useful.
- Inspect data for artifacts (motion, eddy currents, susceptibility distortions). Preprocessing—motion and eddy current correction, susceptibility distortion correction—is often required. You can use FSL (eddy/topup), MRtrix3, or other packages before importing into DSI Studio.
- In DSI Studio you can create a .src file from the diffusion data (File → Reconstruct → Create .src) by supplying the diffusion-weighted images, bval, and bvec. The .src format stores diffusion signals and metadata for faster processing in DSI Studio.
Practical tips:
- Ensure bvecs are in the same coordinate system as images; misaligned bvecs cause incorrect reconstructions.
- If your data include reversed phase-encode pairs for susceptibility correction, do that before creating .src or reconstructing.
Reconstruction methods in DSI Studio
DSI Studio supports several reconstruction approaches. For beginners, two commonly used options are:
-
Generalized Q-sampling Imaging (GQI)
- Pros: Works with single-shell and multi-shell data; robust for tractography; computes quantitative anisotropy (QA).
- Use case: Most general-purpose tractography pipelines in DSI Studio.
-
Q-ball Imaging (QBI)
- Pros: Good angular resolution from high angular sampling schemes.
- Use case: Data with many gradient directions, moderate b-values.
Other options include DTI (limited for complex fiber crossings), Diffusion Spectrum Imaging (DSI) for grid-sampled q-space, and multi-shell model fits. Choose based on your acquisition.
Reconstruction in DSI Studio:
- Open the .src file (File → Open).
- Click Reconstruct and select the reconstruction method (e.g., GQI).
- Set reconstruction parameters: isotropic resolution, ODF smoothing, ratio for GQI, etc.
- Run reconstruction to produce a .fib file (compact representation of ODFs and QA).
Tractography basics
Deterministic tractography in DSI Studio propagates streamlines by stepping from voxel to voxel following the local peak direction of the ODF/QA. Basic parameters to set:
- Seed region: Where streamlines start. Can be whole-brain (seed voxels across white matter) or ROI-based.
- Seed count: Number of seeds; higher yields denser tractograms but increases processing time.
- Step size: Distance moved per step (usually < voxel size); smaller step sizes follow curvature better.
- Angular threshold (turning angle): Limits how sharply a streamline may bend between steps.
- QA or FA threshold: Stopping criterion—streamlines stop where anisotropy falls below threshold (helps prevent entering gray matter/CSF).
- Minimum/maximum length: Filters short or overly long streamlines.
Typical workflow:
- Load .fib file.
- Choose tractography — select deterministic/probabilistic.
- Set tracking parameters (seed count, thresholds, step size, angular threshold).
- Define ROIs for inclusion/exclusion if targeted tracts are desired.
- Run tracking to produce streamlines and inspect them in the 3D viewer.
Example recommended starter settings for whole-brain deterministic tracking:
- Seed count: 1,000,000 (or 200,000 for testing)
- Step size: 0.5–1.0 mm
- Angular threshold: 45–60 degrees
- QA threshold: auto or 0.06–0.1 (depends on data)
- Min length: 20 mm, max length: 250 mm
ROI-based tractography and logical operations
ROI-driven tractography refines tract selection:
- Seed ROI: limit seeds to a mask (e.g., left precentral gyrus).
- Include ROI(s): streamlines must pass through these regions.
- Exclude ROI(s): streamlines passing through these are discarded.
DSI Studio supports Boolean logic for ROIs (AND, OR, NOT) and interactive drawing tools. For example, to extract the corticospinal tract, place ROIs in the posterior limb of the internal capsule and cerebral peduncle and use an inclusion rule (AND) with exclusion masks to remove spurious fibers.
Visualizing and cleaning tractograms
DSI Studio’s viewer allows coloring by orientation, QA, or scalar metrics (FA, AD, RD, MD if available). Use interactive clipping planes, fiber selection tools, and ROI filters to refine results.
To clean spurious fibers:
- Use manual ROI exclusions.
- Use clustering and fiber number thresholds to remove small isolated clusters.
- Use “Remove Short/Long Fibers” functions and “Group fibers” to identify major bundles.
Quantification and connectomics
Quantitative analyses possible in DSI Studio:
- Extract scalar values (QA, FA, AD, RD) along fibers or within ROIs.
- Fiber counts and density, mean length.
- Connectome construction: Define a parcellation (e.g., AAL, Desikan) as nodes and compute connectivity matrices weighted by fiber count, density, or mean QA along tracts.
Export options include tract files (.trk/.tck), connectivity matrices (CSV), and images.
Example: to compute a connectome:
- Load .fib and parcellation NIfTI aligned to diffusion space.
- Use the Connectometry → Connectome function to set nodes and edge weighting.
- Export the adjacency matrix for statistical analysis.
Common pitfalls and troubleshooting
- Misoriented bvecs: produces incorrect fiber orientations. Check with visualization of principal directions.
- Insufficient angular resolution (too few directions): crossing fibers will be poorly resolved.
- Inadequate preprocessing: motion and distortions can corrupt reconstructions—apply eddy/topup or equivalent.
- Overaggressive tracking parameters: too low QA/FA threshold or large angular threshold yields many false positives.
- Over-reliance on streamline counts as direct measure of connectivity—streamline counts are influenced by tracking parameters and seeding strategy; prefer normalized measures or microstructural weighting.
Example beginner pipeline (concise)
- Preprocess: DICOM → NIfTI; run motion/eddy/susceptibility correction.
- Create .src in DSI Studio with images, bvals, bvecs.
- Reconstruct with GQI to produce .fib.
- Whole-brain deterministic tracking (200k seeds) to inspect general anatomy.
- Define ROIs and run targeted tractography with 100k–1M seeds.
- Clean tractogram with exclusion ROIs and clustering.
- Quantify metrics along tracts; export results.
Practical tips
- Start with smaller seed counts for interactive tuning, then scale up for final analyses.
- Save parameter presets once you find reliable settings for reproducibility.
- Document preprocessing steps, exact tracking parameters, ROI definitions, and software versions.
- Validate extracted tracts against known anatomy and, if possible, across subjects.
Resources for learning
- DSI Studio’s built-in help and example datasets.
- Published method papers on GQI and tractography best practices.
- Online tutorials and community forums for practical tips and example parameter sets.
Conclusion
DSI Studio provides a flexible platform for diffusion MRI reconstruction and tractography that balances advanced algorithms with an accessible interface. For beginners, focus on careful preprocessing, choosing an appropriate reconstruction method (GQI is a good general choice), iterative parameter tuning with small seed counts, and validating tract outputs anatomically. Keep records of parameters and workflow for reproducibility.