DMRIPrep modules

Modules of the preprocessing and quality control pipeline. A protocol lists the modules to run and the value of each of their options; dmriprep make-protocols writes one with the defaults below.

Module	Purpose	Options
BASELINE_Average	Averaging baselines of the diffusion weighted image	5
BRAIN_Mask	Brain Masking, mask file will be added to the global variables in the result file	16
BRAIN_Tractography	Brain tractography (whole/single region) using DIPY library	17
DTI_Estimate	Estimate DTI	3
DTI_Register	Register DTI to the fixed volume using DTIReg	28
DWI_Denoise	Denoising of the DWI with DIPY (MP-PCA or Patch2Self). Use it first in the pipeline, on the raw images, before any interpolation and before GIBBS_Correct	3
EDDYMOTION_Correct	Eddy Motion correction, supporting single image eddy correction as well as with susceptibility correction	5
GIBBS_Correct	Gibbs ringing removal with DIPY (local subvoxel shifts, the method of MRtrix mrdegibbs) for full Fourier acquisitions. Use it after DWI_Denoise and before any interpolation	2
IDENTITY_Process	Just pass image to the next module, use this as converter (nrrd <-> nifti)	1
IMAGE_Filter	Custom module	4
INTERLACE_Check	Interlaced correlation check across the gradient volumes	6
MANUAL_Exclude	Manually excludes gradient volumes	1
MULTI_SHELL_Estimate	MULTI_SHELL Estimate	8
QC_Report	Generating report documents	4
SLICE_Check	Slicewise correlation check to exclude problematic gradient volumes	8
SUSCEPTIBILITY_Correct	Susceptibility correction with FSL, 2 phase-encoded images are required to use this module	3
UTIL_Merge	Merging two diffusion images to one	1