DTI pre-processing

Diffusion Tensor Imaging depicts the anisotropy of tissue.

The acquisition protocol includes 6 or more diffusion weighted images (DWIs), one or more B null image (B0), a structural T1 image (eventually a brain mask), and sometimes field maps (FM) that are used for susceptibility correction.

The nipype script to generate the DTI is perform_dti_processing.py and its help message is the following:

usage: perform_dti_processing.py [-h] -i dwis [dwis ...] -a bvals [bvals ...]
                                 -e bvecs [bvecs ...] -t t1 [-m fieldmapmag]
                                 [-p fieldmapphase] [-o output_dir] [-g]
                                 [--rot rot] [--etd etd] [--ped [ped]]
                                 [--rigid]

Perform Diffusion Model Fitting with pre-processing steps. Mandatory Inputs
are the Diffusion Weighted Images and the bval/bvec pair. as well as a T1
image are extracted for reference space. The Field maps are provided so
susceptibility correction is applied. Values to use for the susceptibility
parameters: ## DRC ## (--ped=-y --etd=2.46 --rot=34.56) and ## 1946 ##
(--ped=-y --etd=2.46 --rot=25.92). Note that these values are indicative.

optional arguments:
  -h, --help            show this help message and exit
  -i dwis [dwis ...], --dwis dwis [dwis ...]
                        Diffusion Weighted Images in a 4D nifti file
  -a bvals [bvals ...], --bvals bvals [bvals ...]
                        bval file to be associated with the DWIs
  -e bvecs [bvecs ...], --bvecs bvecs [bvecs ...]
                        bvec file to be associated with the DWIs
  -t t1, --t1 t1        T1 file to be associated with the DWIs
  -m fieldmapmag, --fieldmapmag fieldmapmag
                        Field Map Magnitude image file to be associated with
                        the DWIs
  -p fieldmapphase, --fieldmapphase fieldmapphase
                        Field Map Phase image file to be associated with the
                        DWIs
  -o output_dir, --output_dir output_dir
                        Output directory containing the registration result
                        Default is a directory called results
  -g, --graph           Print a graph describing the node connections
  --rot rot             Diffusion Read-Out time used for susceptibility
                        correction Default is 34.56
  --etd etd             Echo Time difference used for susceptibility
                        correction Default is 2.46
  --ped [ped]           Phase encoding direction used for susceptibility
                        correction (x, y or z) --ped=val form must be used for
                        -ve indicesDefault is the -y direction (-y)
  --rigid               Only use rigid registration for DWI (no eddy current
                        correction)