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Generate5tt2gmwmi brick

Generate a mask image appropriate for seeding streamlines on the grey matter-white matter interface

(mrtrix 5tt2gmwmi command)


Mandatory inputs parameters:

  • in_file (a string representing an existing file)

    Input 5TT segmented anatomical image (valid extensions: [.mif, .nii, .nii.gz]). From Generate5ttfsl brick for example.

    ex. '/home/username/data/raw_data/T1w_5tt.mif'
    

Optional inputs parameters:

  • in_mask (a string representing an existing file)

    Filter an input mask image (valid extensions: [.mif, .nii, .nii.gz]) according to those voxels that lie upon the grey matter - white matter boundary.

    If no input mask is provided, the output will be a whole-brain mask image calculated using the anatomical image only.

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

Outputs parameters:

  • out_file (a pathlike object or string representing a file)

    The output mask image.

    ex. '/home/username/data/derived_data/T1w_5tt_gmwmSeed.mif'
    

Useful links:

mrtrix 5tt2gmwmi