Take an AFNI-style DT file as input, such as might be output by 3dDWItoDT (which means that the DT elements are ordered: Dxx,Dxy,Dyy,Dxz,Dyz,Dzz), as well as a set of gradients, and then generate a synthetic set of DWI measures with a given SNR. Might be useful for simulations/testing.
Part of FATCAT (Taylor & Saad, 2013) in AFNI. It is similar in premise to 3dDTtoDWI, however this allows for the modeled inclusion of Rician noise (such as appears in MRI magnitude images).
- COMMAND: 3dDTtoNoisyDWI -dt_in DTFILE -grads GRADFILE -noise_frac0 FF
{-bval BB} {-S0 SS} {-mask MASK } -prefix PREFIX
1) If N gradients are input, then the output is a file with N+1 bricks that mimics a set of B0+DWI data (0th brick is the B0 reference).
RUNNING: -dt_in DTFILE :diffusion tensor file, which should have six bricks
of DT components ordered in the AFNI (i.e., 3dDWItoDT) manner: Dxx,Dxy,Dyy,Dxz,Dyz,Dzz.
It is assumed that there is no row of all zeros in the GRADFILE (i.e., representing the b=0 line). If there are N rows in GRADFILE, then the output DWI file will have N+1 bricks (0th will be the b=0 reference set of noise S0 measures).
- -noise_DWI FF :fractional value of noise in DWIs. The magnitude will
- be set by the b=0 reference signal, S0. Rician noise is used, which is characterized by a standard deviation, sigma, so that FF = sigma/S0 = 1/SNR0. For example, FF=0.05 roughly corresponds to an SNR0=20 ‘measurement’.
- -noise_B0 FF2 :optional switch to use a different fraction of Rician
- noise in the b=0 reference image; one might consider it realistic to have a much lower level of noise in the reference signal, S0, mirroring the fact that generally multiple averages of b=0 acquisitions are averaged together. If no fraction is entered here, then the simulation will run with FF2=FF.
- -prefix PREFIX :output file name prefix. Will have N+1 bricks when
- GRADFILE has N rows of gradients.
-mask MASK :can include a mask within which to calculate uncert. Otherwise, data should be masked already.
- -bval BB :optional DW factor to use if one has DT values scaled
- to something physical (NB: AFNI 3dDWItoDT works in a world of b=1, so the default setting here is BB=1; one probably doesn’t need to change this if using DTs made by 3dDWItoDT).
- -S0 SS :optional reference b=0 signal strength. Default value
- SS=1000. This just sets scale of output.
EXAMPLE: 3dDTtoNoisyDWI
-dti_in DTI/DT_DT+orig -grads GRADS.dat -noise_DWI 0.1 -noise_B0 0 -prefix NEW_DWIs_SNR10
If you use this program, please reference the introductory/description paper for the FATCAT toolbox:
Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional And Tractographic Connectivity Analysis Toolbox. Brain Connectivity 3(5):523-535.