DWIBrainMask brick¶
Generates a whole brain mask from a DWI image.¶
All diffusion weighted and b=0 volumes are used to obtain a mask that includes both brain tissue and CSF.
(mrtrix dwi2mask 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 nputs parameters:
- in_file (a pathlike object or a string representing an existing file)
Input DWI image (valid extensions: [.mif]).
ex. ['/home/username/data/raw_data/DWI.mif']
Outputs parameters:
- out_file (a pathlike object or string representing a file)
Output brain mask.
ex. '/home/username/data/derived_data/DWI_brainmask.mif'
Useful links: