【MRtrix】 MRtrixを用いた拡散テンソルイメージング: DTI

SYNOPSIS

     Diffusion (kurtosis) tensor estimation

USAGE

     dwi2tensor [ options ] dwi dt

        dwi          the input dwi image.

        dt           the output dt image.


DESCRIPTION

     By default, the diffusion tensor (and optionally its kurtosis) is fitted
     to the log-signal in two steps: firstly, using weighted least-squares
     (WLS) with weights based on the empirical signal intensities; secondly, by
     further iterated weighted least-squares (IWLS) with weights determined by
     the signal predictions from the previous iteration (by default, 2
     iterations will be performed). This behaviour can be altered in two ways:

     * The -ols option will cause the first fitting step to be performed using
     ordinary least-squares (OLS); that is, all measurements contribute equally
     to the fit, instead of the default behaviour of weighting based on the
     empirical signal intensities.

     * The -iter option controls the number of iterations of the IWLS
     prodedure. If this is set to zero, then the output model parameters will
     be those resulting from the first fitting step only: either WLS by
     default, or OLS if the -ols option is used in conjunction with -iter 0.

     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

  -ols
     perform initial fit using an ordinary least-squares (OLS) fit (see
     Description).

  -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 for IWLS algorithm (default: 2) (see
     Description).

  -predicted_signal image
     the predicted dwi image.

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.

Standard options

  -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.

SYNOPSIS

     Generate maps of tensor-derived parameters

USAGE

     tensor2metric [ options ] tensor

        tensor       the input tensor image.


OPTIONS

  -adc image
     compute the mean apparent diffusion coefficient (ADC) of the diffusion
     tensor. (sometimes also referred to as the mean diffusivity (MD))

  -fa image
     compute the fractional anisotropy (FA) of the diffusion tensor.

  -ad image
     compute the axial diffusivity (AD) of the diffusion tensor. (equivalent to
     the principal eigenvalue)

  -rd image
     compute the radial diffusivity (RD) of the diffusion tensor. (equivalent
     to the mean of the two non-principal eigenvalues)

  -cl image
     compute the linearity metric of the diffusion tensor. (one of the three
     Westin shape metrics)

  -cp image
     compute the planarity metric of the diffusion tensor. (one of the three
     Westin shape metrics)

  -cs image
     compute the sphericity metric of the diffusion tensor. (one of the three
     Westin shape metrics)

  -value image
     compute the selected eigenvalue(s) of the diffusion tensor.

  -vector image
     compute the selected eigenvector(s) of the diffusion tensor.

  -num sequence
     specify the desired eigenvalue/eigenvector(s). Note that several
     eigenvalues can be specified as a number sequence. For example, '1,3'
     specifies the principal (1) and minor (3) eigenvalues/eigenvectors
     (default = 1).

  -modulate choice
     specify how to modulate the magnitude of the eigenvectors. Valid choices
     are: none, FA, eigval (default = FA).

  -mask image
     only perform computation within the specified binary brain mask image.

Standard options

  -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.