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Dwi_preprocessing pipeline

DWI preprocessing using a reverse-phase encoded b0

The aim of this pipeline is to preprocess a multishell diffusion data before to analysed it. In this pipeline, an image with b=0 volumes with opposite phase encoding should be provided for the purpose of EPI distortion correction.

The following steps are done:

- denoise the image and estimate the spatially varying noise map

- remove Gibb’s ringing artefacts

- motion and distortion correction (EPI-distrortion correction, B0-field inhomogeneity correction, Eddy-current and movement distortion correction )

- bias field correction

A binary mask of the brain is also estimated.

The outputs are in “.mif” format.

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Pipeline insight

Dwi_preprocessing pipeline combines the following bricks:

- Conversion into MIF format (if NIfTI provided)

- b0 extraction

- b0 averaging

- b0 concatenation

- Denoising

- Unringing

- Motion distorstion correction (Topup and eddy correction) (default values: rpe_options = “pair”, eddy_options = “ –slm=linear –data_is_shelled”)

- Bias correction

- Brain mask estimation

Mandatory inputs parameters

• in_dwi (a string representing an existing file)

  Diffusion image to preprocess (valid extensions: [.nii, .nii.gz, ‘.mif’]). If a NIfTI is supplied, bvec and bval files will be found automatically.

  ex. '/home/username/data/raw_data/DWI.nii'
  

• in_dwi_pe_dir (ap, pa, lr, rl, default value is ap, optional)

  Phase encoding direction of the in_diw image:

  - ap : Anterior to posterior

  - pa: Posterior to anterior

  - lr: Left to right

  - rl: Right toleft

  ex. ap
  

• in_dwi_ro_time (a float, optional)

  Total readout time of in_dwi image (in seconds).

  ex. 2.0
  

• in_b0_reverse (a string representing an existing file)

  b=0 volumes with opposing phase-direction which is to be used exclusively by topup for estimating the inhomogeneity field (valid extensions: [.nii, .nii.gz, ‘.mif’]).

  ex. '/home/username/data/raw_data/b0_reverse.nii'
  

Outputs parameters:

• brain_mask

  DWI brain mask image.

  ex. '/home/username/data/derived_data/DWI_denoised_unringed_dwifslpreproc_unbias_brain_mask.mif'
  

• preproc_dwi

  DWI corrected image.

  ex. '/home/username/data/derived_data/DWI_denoised_unringed_dwifslpreproc_unbias.mif'