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.
A binary mask of the brain is also estimated.
The outputs are in “.mif” format.
Pipeline insight
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'