xfibres function

Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers

Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques with Crossing Fibers

Calls xfibres from FSL to fit, also known as bedpostx

xfibres( infile, bvecs, bvals, mask = NULL, nfibres = 1, bet.opts = "", verbose = TRUE, njumps = NULL, burnin = NULL, burnin_noard = NULL, sampleevery = NULL, updateproposalevery = NULL, seed = NULL, noard = FALSE, allard = FALSE, nospat = FALSE, nonlinear = FALSE, cnonlinear = FALSE, rician = FALSE, f0 = FALSE, ardf0 = FALSE, opts = "" )

Arguments

  • infile: Input filename
  • bvecs: b-vectors: matrix of 3 columns or filename of ASCII text file
  • bvals: b-values: vector of same length as number of rows of b-vectors or filename of ASCII text file
  • mask: Mask filename
  • nfibres: Maximum number of fibres to fit in each voxel (default 1)
  • bet.opts: Options for fslbet if mask is not supplied
  • verbose: print diagnostic messages
  • njumps: num of jumps to be made by MCMC (default is 5000)
  • burnin: Total num of jumps at start of MCMC to be discarded (default is 0)
  • burnin_noard: num of burnin jumps before the ard is imposed (default is 0)
  • sampleevery: num of jumps for each sample (MCMC) (default is 1)
  • updateproposalevery: num of jumps for each update to the proposal density std (MCMC) (default is 40)
  • seed: for pseudo random number generator
  • noard: Turn ARD off on all fibres
  • allard: Turn ARD on on all fibres
  • nospat: Initialise with tensor, not spatially
  • nonlinear: Initialise with nonlinear fitting
  • cnonlinear: Initialise with constrained nonlinear fitting
  • rician: Use Rician noise modelling
  • f0: Add to the model an unattenuated signal compartment
  • ardf0: Use ard on f0
  • opts: Additional options for xfibres. There should not be any left out in the current arguments, but opts may be a way some prefer to input options.

Returns

Output from system

  • Maintainer: John Muschelli
  • License: GPL-3
  • Last published: 2024-05-10

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