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. .. list-table:: :header-rows: 1 :widths: 25 60 15 * - Module - Purpose - Options * - :doc:`BASELINE_Average ` - Averaging baselines of the diffusion weighted image - 5 * - :doc:`BRAIN_Mask ` - Brain Masking, mask file will be added to the global variables in the result file - 16 * - :doc:`BRAIN_Tractography ` - Brain tractography (whole/single region) using DIPY library - 17 * - :doc:`DTI_Estimate ` - Estimate DTI - 3 * - :doc:`DTI_Register ` - Register DTI to the fixed volume using DTIReg - 28 * - :doc:`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 * - :doc:`EDDYMOTION_Correct ` - Eddy Motion correction, supporting single image eddy correction as well as with susceptibility correction - 5 * - :doc:`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 * - :doc:`IDENTITY_Process ` - Just pass image to the next module, use this as converter (nrrd <-> nifti) - 1 * - :doc:`IMAGE_Filter ` - Custom module - 4 * - :doc:`INTERLACE_Check ` - Interlaced correlation check across the gradient volumes - 6 * - :doc:`MANUAL_Exclude ` - Manually excludes gradient volumes - 1 * - :doc:`MULTI_SHELL_Estimate ` - MULTI\_SHELL Estimate - 8 * - :doc:`QC_Report ` - Generating report documents - 4 * - :doc:`SLICE_Check ` - Slicewise correlation check to exclude problematic gradient volumes - 8 * - :doc:`SUSCEPTIBILITY_Correct ` - Susceptibility correction with FSL, 2 phase-encoded images are required to use this module - 3 * - :doc:`UTIL_Merge ` - Merging two diffusion images to one - 1 .. toctree:: :maxdepth: 1 :hidden: dmriprep/BASELINE_Average dmriprep/BRAIN_Mask dmriprep/BRAIN_Tractography dmriprep/DTI_Estimate dmriprep/DTI_Register dmriprep/DWI_Denoise dmriprep/EDDYMOTION_Correct dmriprep/GIBBS_Correct dmriprep/IDENTITY_Process dmriprep/IMAGE_Filter dmriprep/INTERLACE_Check dmriprep/MANUAL_Exclude dmriprep/MULTI_SHELL_Estimate dmriprep/QC_Report dmriprep/SLICE_Check dmriprep/SUSCEPTIBILITY_Correct dmriprep/UTIL_Merge