Generates a whole brain mask from a DWI image
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
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.
- -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.
- -info display information messages.
- -quiet do not display information messages or progress status; alternatively, this can be achieved by setting the MRTRIX_QUIET environment variable to a non-empty string.
- -debug display debugging messages.
- -force force overwrite of output files (caution: using the same file as input and output might cause unexpected behaviour).
- -nthreads number use this number of threads in multi-threaded applications (set to 0 to disable multi-threading).
- -config key value (multiple uses permitted) temporarily set the value of an MRtrix config file entry.
- -help display this information page and exit.
- -version display version information and exit.
Dhollander T, Raffelt D, Connelly A. Unsupervised 3-tissue response function estimation from single-shell or multi-shell diffusion MR data without a co-registered T1 image. ISMRM Workshop on Breaking the Barriers of Diffusion MRI, 2016, 5
Tournier, J.-D.; Smith, R. E.; Raffelt, D.; Tabbara, R.; Dhollander, T.; Pietsch, M.; Christiaens, D.; Jeurissen, B.; Yeh, C.-H. & Connelly, A. MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation. NeuroImage, 2019, 202, 116137
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