DWI data simulation

Generate DWI data from a configuration file

We provides DWISimulator routine to generate DWI data from a customizable configuration file. See example codes in Example/test.sh and example configuration files in Example folder.

See userguide.

Generate data with 3 shells.

export DMRITOOL_EXAMPLE_DIR=${DMRITOOL_SOURCE_DIR}/Examples

b=1000,2000,3000
DWISimulator ${DMRITOOL_EXAMPLE_DIR}/dwi_crossing.txt --outdwi dwi.nii.gz --outodf odfTrue.nii.gz --outeap eapTrue_r0.015.nii.gz --qorientations ${DMRITOOL_EXAMPLE_DIR}/Elec060.txt --bvalues ${b} --rorientations ${DMRITOOL_EXAMPLE_DIR}/directions_t4.txt --rvalues 0.015 --noisesigma 0.0 --outb0 dwi_diagonal_b0.nii.gz --outputdwitype EACHSHELL
  • It uses the same gradient file ${DMRITOOL_EXAMPLE_DIR}/Elec060.txt for these three shells.
  • If you want to use different gradient files in different shell, try to use --bfile to specifically set b values for each gradient direction.
  • The routine will output a dwi.txt file (same name as dwi.nii.gz). The file contains three shells separately in three lines, because we set --outputdwitype EACHSHELL. --outputdwitype 4DALL will generate one dwi data file, one gradient file and one b value file for all 180 DWI volumes.

The ground truth of EAP profile field with radius 15 \mu m is in eapTrue_r0.015.nii.gz, and the ground truth ODF file is odfTrue.nii.gz. The you can visualize the ground truth of EAP profiles and ODFs via vtkviewer, VTKPolyData.py or via Paraview.

MeshFromSphericalFunctionTessellatedSamples eapTrue_r0.015.nii.gz eapTrue_r0.015_vis.vtk ${DMRITOOL_EXAMPLE_DIR}/directions_t4.txt  --scale 8e-6
VTKPolyData.py --vtk eapTrue_r0.015_vis.vtk --png eapTrue_r0.015.png  --zoom 1.3
eapTrue_r0.015.png

eapTrue_r0.015

MeshFromSphericalFunctionTessellatedSamples odfTrue.nii.gz odfTrue_vis.vtk ${DMRITOOL_EXAMPLE_DIR}/directions_t4.txt  --scale 1.5
VTKPolyData.py --vtk odfTrue_vis.vtk --png odfTrue.png --zoom 1.3
odfTrue.png

odfTrue

To obtain the ground truth of MSD map, RTO map, you can use:

b=1000,2000,3000
DWISimulator ${DMRITOOL_EXAMPLE_DIR}/dwi_crossing.txt --outdwi dwi.nii.gz --outodf odfTrue.nii.gz --outeap eapTrue_r0.015.nii.gz --outrto rtoTrue.nii.gz --outmsd msdTrue.nii.gz --qorientations ${DMRITOOL_EXAMPLE_DIR}/Elec060.txt --bvalues ${b} --rorientations ${DMRITOOL_EXAMPLE_DIR}/directions_t4.txt --rvalues 0.015 --noisesigma 0.0 --outb0 dwi_diagonal_b0.nii.gz --outputdwitype EACHSHELL

You can also add noise to the noise-free dwi data.

DWINoiseGenerator dwi_b1000.nii.gz  dwi_b1000_noise.nii.gz --snr 25

--snr 25 means variance of the noise is S(0)/25, if b0 image is not set by --b0, then S(0)=1 is the default value.