【MRtrix】MRtrixを用いた拡散MRIのマスク画像の作成

SYNOPSIS

     Generates a whole brain mask from a DWI image

USAGE

     dwi2mask [ options ] input output

        input        the input DWI image containing volumes that are both
                     diffusion weighted and b=0

        output       the output whole-brain mask image


DESCRIPTION

     All diffusion weighted and b=0 volumes are used to obtain a mask that
     includes both brain tissue and CSF.

     In a second step peninsula-like extensions, where the peninsula itself is
     wider than the bridge connecting it to the mask, are removed. This may
     help removing artefacts and non-brain parts, e.g. eyes, from the mask.

OPTIONS

  -clean_scale value
     the maximum scale used to cut bridges. A certain maximum scale cuts
     bridges up to a width (in voxels) of 2x the provided scale. Setting this
     to 0 disables the mask cleaning step. (Default: 2)

DW gradient table import options

  -grad file
     Provide the diffusion-weighted gradient scheme used in the acquisition in
     a text file. This should be supplied as a 4xN text file with each line is
     in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the
     applied gradient, and b gives the b-value in units of s/mm^2. If a
     diffusion gradient scheme is present in the input image header, the data
     provided with this option will be instead used.

  -fslgrad bvecs bvals
     Provide the diffusion-weighted gradient scheme used in the acquisition in
     FSL bvecs/bvals format files. If a diffusion gradient scheme is present in
     the input image header, the data provided with this option will be instead
     used.