Diffusion Models and Metrics
Before practicum on Friday, please complete following:
- Read [5. Fiber resolving methods]
- 5.1. Model-based methods
- 5.2. Model-free methods
- 5.3. Spherical deconvolution
- 5.4. Comparison
- Watch a video about diffusion tensor imaging
During practicum on Friday:
Diffusion MRI models
- Diffusion Models
- Model-based methods (DTI, FSL’s BSM, DKI, NODDI)
- Model-free methods (DSI Studio’s GQI)
- Spherical deconvolution methods (MRtrix’s CSD, MSMT-CSD)
Model/Method | B-table requirements | Handle Free Water | Quantify Restricted Diffusion | Resolve Multiple Fibers | Metrics |
---|---|---|---|---|---|
DTI | B0, >= 1 b-value(s) | No (except for DTI-FWE) | No | No (except for Multi-Tensor) | fa, ad, rd, md |
DKI | B0, >= 2 b-values | Yes | Yes | No (except for Multi-Tensor) | ak, rk, mk |
NODDI | B0, >= 2 b-values | Yes | Yes | No (except for Multi-Fiber NODDI ) | iso, odi, ndi (icvf) |
GQI | B0, >= 1 b-value(s) | Yes | Yes | Yes | qa, iso, rdi |
CSD | 1 b-value | No | No | Yes | afd |
CSD-MSMT | >= 2 b-values | Yes | Yes | Yes | afd |
- Metrics
- Voxel-based metrics
- Fiber-based metrics
- Tractography-based metrics: connectivity, (shape metrics)
- Graph-based metrics: network measures
- Interpretation
- Fiber integrtity:
- axonal density: fa, qa, afd, odi, ad, SIFT connectivity
- myelination: fa, rd, qa
- Cellularity: rdi, ndi, md,
- Free water: iso, fw
- Fiber integrtity:
Hands-on: DTI, GQI, and QSDR Reconstruction
- Download control subject 1 session 1 data from the SCA2 Diffusion Tensor Imaging study
- Reconstruction using DRI, GQI, QSDR
- Check and compare FIB files
- Batch SRC reconstruction
Hands-on: dMRI analysis
- Region-based analysis
- Use [Region][Statistics] to get diffusion metrics from atlases (Documentation).
- Tract-based analysis
- Map corticospinal tracts
- Get diffusion metrics at CST using [Tracts][Statistics]
- Use tract cutting (with selection & separate deleted tract) to segment CST into segments above internal capsule (IC), IC, and below IC sections.
- Plot along CST metrics at z-direction or fiber direction. (Documentation)
- Region-based and Tract-based analysis using connectometry database
- Create connectometry DB
- Connectometry DB samples
- Region-based analysis
- Tract-based analysis
Practicum assignment: ROI-based and Track-based analysis comparing SCA2 with controls
- Download the SCA2 Diffusion Tensor Imaging study
- Reconstruct data at [Step T2 Reconstruction] using QSDR
- Create connectometry databases using [Step C2: Create a connectometry Database], one for
nqa
, and one forfa
. - Open the database at [Step T3: Fiber Tracking]
- Use region-based analysis to get metrics (nqa, fa) from patients and controls and compare.
- Use tract-based analysis to get metrics (nqa, fa) from patients and controls and compare.
- Segment CST into segmentation to get metrics (nqa, fa) and compare them between patients and controls.