Diffusion MRI Basics

Before practicum on Friday, please complete following:

Diffusion MRI basics



During practicum on Friday:

Overview (10 min)

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 sensitization (5 min)

Sampling schemes of the b-table (5 min)

image

Quality Checks on dMRI data

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

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

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

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

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

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.