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

Hands-on: DTI, GQI, and QSDR Reconstruction

• Download control subject 1 session 1 data from the SCA2 Diffusion Tensor Imaging study
  • BVAL
  • BVEC
  • NIFTI
• 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

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Practicum assignment: ROI-based and Track-based analysis comparing SCA2 with controls

1. Download the SCA2 Diffusion Tensor Imaging study
2. Reconstruct data at [Step T2 Reconstruction] using QSDR
3. Create connectometry databases using [Step C2: Create a connectometry Database], one for nqa, and one for fa.
4. Open the database at [Step T3: Fiber Tracking]
5. Use region-based analysis to get metrics (nqa, fa) from patients and controls and compare.
6. Use tract-based analysis to get metrics (nqa, fa) from patients and controls and compare.
7. Segment CST into segmentation to get metrics (nqa, fa) and compare them between patients and controls.