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
- 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
During practicum on Friday:
Diffusion MRI Basics
- 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
- Hands-on: create SRC files from NIFTI data
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
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)
- Hands-on
-
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
- Hands-on
Assignment :
Process dMRI data on real-world studies
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Download data from the SCA2 Diffusion Tensor Imaging study to a folder (e.g. D:/SCA2) study
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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).
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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)
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Check the report and identify scan with problematic data.
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Open the problematic SRC file in [Step T2 Reconstruction] and identify the cause.
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Apply eddy correction and compare the quality control report with/without correction.