Diffusion MRI Basics

Before practicum on Friday, please complete following:

Diffusion MRI basics

• Read [4. Diffusion MRI acquisitions]
  • 4.1. Scanning time
  • 4.2. B-value
  • 4.3. Sampling scheme
• Watch a video about dMRI

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• Read [4.4 Distortions and artifacts]
  • 4.4.1. Eddy current distortion
  • 4.4.2. Susceptibility-induced distortions and artifacts
• Watch a video about distortions and artifacts in dMRI

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During practicum on Friday:

Diffusion MRI Basics

source: Morozov, Sergey, et al. “Diffusion processes modeling in magnetic resonance imaging.” Insights into Imaging 11.1 (2020): 1-9.

• B-value: Diffusion sensitization
  • Diffusion time (Δ)
  • Diffusion gradient strength (g)
  • Diffusion gradient duration (δ)

  

  (γ: gyromagnetic ratio)

• B-vector: Diffusion encoding directions
• Apparent diffusion coefficient

source: Morozov, Sergey, et al. “Diffusion processes modeling in magnetic resonance imaging.” Insights into Imaging 11.1 (2020): 1-9.

• Hands-on: create SRC files from NIFTI data
  • sub-01_run-1_dwi.nii.gz
  • sub-01_run-1_dwi.bval
  • sub-01_run-1_dwi.bvec
  • source: Datasets with and without deliberate head movements for detection and imputation of dropout in diffusion MRI
  • Create an SRC file

Sampling schemes of the b-table

• Single-shell: one b-value at 30 directions (e.g. DTI, high angular resolution diffusion imaging, a.k.a. HARDI)
• Multi-shell: 2 or 3 b-values with 90 directions acquired at each b-value
• Grid: a total of 258 directions acquired by 23 b-values.

• Hands-on: identify sampling schemes
  • Single-shell
  • Multi-Shell
  • Grid

Quality Checks on dMRI data

• Motion artifacts and eddy distortion
  • Hands-on
    • sub-01_run-2_dwi.nii.gz
    • sub-01_run-2_dwi.bval
    • sub-01_run-2_dwi.bvec
    • source: Datasets with and without deliberate head movements for detection and imputation of dropout in diffusion MRI
    • Identify motion induced signals issues
  • Motion artifacts
    • often has slice signal dropout

    

    (source: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy)

    • Correction using FSL’s eddy

  • Eddy current distortion

    • Larger with higher b-value
    • Can be corrected in the MRI sequence to cancel eddy currents

    

    (source: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy)

• Susceptibility distortion and artifact

  

  (source: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide)

  • Hands-on
    • sub-01_acq-multiband_dwi.nii.gz
    • sub-01_acq-multiband_dir-PA_dwi.nii.gz
    • sub-01_acq-multiband_dwi.bval
    • sub-01_acq-multiband_dwi.bvec
    • Correct susceptibility artifact and distortion using FSL’s topup

Assignment :

Process dMRI data on real-world studies

1. Download data from the SCA2 Diffusion Tensor Imaging study to a folder (e.g. D:/SCA2) study

2. Click [Batch Processing][Step B2a: NIFTI to SRC (BIDS)] and select the folder. DSI Studio will ask to specify another folder to output the SRC files (e.g. D:/src).

3. Run [Diffusion MRI Analysis][Step T1a: Quality Control] and select the folder storing the SRC files. Save the report as a text file (e.g. report.txt)

4. Check the report and identify scan with problematic data.

5. Open the problematic SRC file in [Step T2 Reconstruction] and identify the cause.

6. Apply eddy correction and compare the quality control report with/without correction.