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:

Overview (10 min)

• 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

CLI for creating SRC

dsi_studio --action=src --source=sub-01_dwi_sub-01_run-1_dwi.nii.gz --bval=sub-01_dwi_sub-01_run-1_dwi.bval --bvec=sub-01_dwi_sub-01_run-1_dwi.bvec --output=sub-01_dwi_sub-01_run-1_dwi.src.gz

Diffusion MRI sequence diagram (10 min)

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

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

• diffusion MRI = MRI acquisition (mostly spin-echo) + additional diffusion sensitization
• diffusion contrast created by signal attenuation

Diffusion sensitization (5 min)

• B-value: a product of variables affecting the sensitivity to diffusion
  • Diffusion time (Δ): the “explosure time”
  • Diffusion gradient strength (g) and duration (δ): the “ISO”

  

  (γ: gyromagnetic ratio)

• B-vector: Diffusion encoding directions

Sampling schemes of the b-table (5 min)

• 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

• 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
  • QC in DSI Studio
• Motion artifacts (5 min)
  • Check sagittal slices
  • Check slice signal dropout
  • Correction using FSL’s eddy
• Eddy distortion (10 min)

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

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

• Linear distortion
• Larger at higher b-value
• Correction using FSL’s eddy
• Bipolar-pulse to cancel eddy currents

CLI for EDDY

dsi_studio --action=rec --source=sub-01_dwi_sub-01_run-1_dwi.nii.gz.src.gz --cmd="[Step T2][Corrections][EDDY]" --save_src=preproc.src.gz

• Susceptibility distortion and artifact (10 min)

(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

CLI for TOPUP+EDDY

dsi_studio --action=rec --source=sub-01_dwi_sub-01_acq-multiband_dwi.nii.gz.src.gz --rev_pe=sub-01_fmap_sub-01_acq-multiband_dir-PA_dwi.nii.gz --save_src=preproc.src.gz

• Recommended steps: TOPUP (handles suscetibility) +EDDY (handles eddy distortion and motion displacement)
  • DWI without reverse PE
    • create SRC from DWI
    • apply eddy: [Step T2][Correction][EDDY]
  • DWI with reverse PE(b0)
    • create SRC from DWI
    • create NIFTI from reversed PE b0
    • apply topup + eddy: [Step T2][Correction][TOPUP/EDDY] or specify –rev_pe=rev_b0.nii.gz
  • DWI with reverse-PE(full DWI)
    • create SRC from DWI
    • create SRC from reversed-PE DWI
    • apply topup + eddy: [Step T2][Correction][TOPUP/EDDY] or specify –rev_pe=rev_dwi.rsrc.gz

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.