DWIExtract brick¶
Extract shell or b=0 volumes from DWI data¶
Extract diffusion-weighted volumes, b=0 volumes or certain shells from a DWI dataset
(mrtrix dwiextract command)
Please note that, in mia_processes, MRtrix bricks required diffusion data in MRtrix .mif format. The MRConvert brick could be used to convert diffusion data in NIfTI format into MRtrix .mif format. In this case, bvec and bval file should be specified.
Mandatory inputs parameters:
- in_file (a string representing an existing file)
Input DWI image (valid extensions: [.mif]).
ex. '/home/username/data/raw_data/DWI.mif'
Optional inputs with default value parameters:
- bzero (a boolean, default value is True, optional)
Extract all b=0 volumes
ex. True
- nobzero (a boolean, default value is False, optional)
Extract all non b=0 volumes
ex. False
- singleshell (a boolean, default value is False, optional)
Force a single-shell (single non b=0 shell) output. This will include b=0 volumes, if present.
Use with bzero option to enforce presence of b=0 volumes (error if not present) or with no_bzero option to exclude them.
ex. False
Optional inputs parameters:
- shell (a list of items which are a float, optional)
Specify one or more gradient shells to use during processing. Default is Undefined (ie parameter not used)
ex. [3000.0]
Outputs parameters:
- out_file (a pathlike object or string representing a file)
The output bias corrected DWI image
ex. '/home/username/data/derived_data/DWI_bzero.mif'
Usefull links: