Diffusion Processing Pipeline for the DRC

This pipeline is performing pre-processing of diffusion data.

The only required input is the DRC-MIDAS 4-5 digit code identifying the acquisition (e.g. -m 1525). You can simpy use the following line to process this pipeline:

perform_dti_processing_drc_protocol.py -m 1525 -o output_dir

The following text describes other optional arguments

usage: perform_dti_processing_drc_protocol.py [-h] -m MIDAS_CODE
                                              [MIDAS_CODE ...] [-o output]
                                              [-r]
                                              [--interpolation INTERPOLATION]
                                              [-g] [--rot rot] [--etd etd]
                                              [--ped [ped]] [--rigid]

Perform Diffusion Model Fitting with pre-processing steps. Mandatory Input is
the 4/5 MIDAS code from which the DWIs, bval bvecs, 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
  -m MIDAS_CODE [MIDAS_CODE ...], --midas_code MIDAS_CODE [MIDAS_CODE ...]
                        MIDAS code of the subject image
  -o output, --output output
                        Result directory where the output data is to be stored
  -r, --resample-t1     Resample the outputs in the T1 space
  --interpolation INTERPOLATION
                        Interpolation options CUB (default) or LIN
  -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)

The outputs are gathered in the -o argument (e.g. output_dir. All output files share a similar prefix in their filename, corresponding to the subject_code.

Here is a list of the principal outputs and their corresponding description:

_corrected_dwi: pre-processed merged diffusion weighted images in a 4D nifti file. (motion, susceptibility, etc)
_corrected_dwi.bval/bvec: corresponding bvalues and gradient vector direction files
_average_b0: the average B-Null image
_dwi_to_b0_rotation.png / _interslice_ncc.png : QC plots describing respectively the subject motion and the signal dropouts throughout the DWI scans
_tensors.nii.gz : output fitted tensor image file, in a 4D format with 6 degrees as a 4th dimension, from which the diffusion based biomarker maps are estimated
_famap : the fractional anisotropy map (3D)
_mdmap : the mean diffusivity map (3D)
_v1map : the first eigen vector component map (3D x 3)
_rgbmap : the directional colour coded RGB FA map.
_mask : mask used to crop background during processing, in the diffusion space
_T1/T2_to_B0.txt : affine transformations between T1/T2 and the average B0 image (with the T1 as reference)