dwi2tensor¶
Description¶
Diffusion (kurtosis) tensor estimation using iteratively reweighted linear least squares estimator.
The tensor coefficients are stored in the output image as follows: volumes 0-5: D11, D22, D33, D12, D13, D23 ; If diffusion kurtosis is estimated using the -dkt option, these are stored as follows: volumes 0-2: W1111, W2222, W3333 ; volumes 3-8: W1112, W1113, W1222, W1333, W2223, W2333 ; volumes 9-11: W1122, W1133, W2233 ; volumes 12-14: W1123, W1223, W1233 ;
Options¶
- -mask image only perform computation within the specified binary brain mask image.
- -b0 image the output b0 image.
- -dkt image the output dkt image.
- -iter integer number of iterative reweightings (default: 2); set to 0 for ordinary linear least squares.
- -predicted_signal image the predicted dwi image.
DW gradient table import options¶
- -grad encoding specify the diffusion-weighted gradient scheme used in the acquisition. The program will normally attempt to use the encoding stored in the image header. 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.
- -fslgrad bvecs bvals specify the diffusion-weighted gradient scheme used in the acquisition in FSL bvecs/bvals format.
- -bvalue_scaling mode specifies whether the b-values should be scaled by the square of the corresponding DW gradient norm, as often required for multi-shell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes/no, true/false, 0/1 (default: true).
Standard options¶
- -info display information messages.
- -quiet do not display information messages or progress status.
- -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)
- -failonwarn terminate program if a warning is produced
- -help display this information page and exit.
- -version display version information and exit.
References¶
Veraart, J.; Sijbers, J.; Sunaert, S.; Leemans, A. & Jeurissen, B. Weighted linear least squares estimation of diffusion MRI parameters: strengths, limitations, and pitfalls. NeuroImage, 2013, 81, 335-346
Author: Ben Jeurissen (ben.jeurissen@uantwerpen.be)
Copyright: Copyright (c) 2008-2016 the MRtrix3 contributors
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MRtrix is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
For more details, see www.mrtrix.org