BEDPOSTX stands for Bayesian Estimation of Diffusion Parameters Obtained
Usage
ni_fsl_bedpostx5(
bvals,
bvecs,
dwi,
mask,
n_fibres,
out_dir,
all_ard = NULL,
args = NULL,
burn_in = 0,
burn_in_no_ard = 0,
cnlinear = NULL,
f0_ard = NULL,
f0_noard = NULL,
force_dir = TRUE,
fudge = NULL,
gradnonlin = NULL,
logdir = NULL,
model = NULL,
n_jumps = 5000,
no_ard = NULL,
no_spat = NULL,
non_linear = NULL,
rician = NULL,
sample_every = 1,
seed = NULL,
update_proposal_every = 40,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- bvals
Character; file path. b values file Required.
- bvecs
Character; file path. b vectors file Required.
- dwi
Character; file path. diffusion weighted image data file Required.
- mask
Character; file path. bet binary mask file Required.
- n_fibres
Character. Maximum number of fibres to fit in each voxel Required.
- out_dir
Character; directory path. output directory Required.
- all_ard
Logical. Turn ARD on on all fibres
- args
Character. Additional parameters to the command
- burn_in
Character. Total num of jumps at start of MCMC to be discarded
- burn_in_no_ard
Character. num of burnin jumps before the ard is imposed
- cnlinear
Logical. Initialise with constrained nonlinear fitting
- f0_ard
Logical. Noise floor model: add to the model an unattenuated signal compartment f0
- f0_noard
Logical. Noise floor model: add to the model an unattenuated signal compartment f0
- force_dir
Logical. use the actual directory name given (do not add + to make a new directory)
- fudge
Integer. ARD fudge factor
- gradnonlin
Logical. consider gradient nonlinearities, default off
- logdir
Character; directory path
- model
Character; one of: "1", "2", "3". use monoexponential (1, default, required for single-shell) or multiexponential (2, multi-shell) model
- n_jumps
Integer. Num of jumps to be made by MCMC
- no_ard
Logical. Turn ARD off on all fibres
- no_spat
Logical. Initialise with tensor, not spatially
- non_linear
Logical. Initialise with nonlinear fitting
- rician
Logical. use Rician noise modeling
- sample_every
Character. Num of jumps for each sample (MCMC)
- seed
Integer. seed for pseudo random number generator
- update_proposal_every
Character. Num of jumps for each update to the proposal density std (MCMC)
- .cwd
Working directory override.
- .env
Named character vector of environment variables.
- .engine
Execution engine override.
- .profile
Runtime profile override.
- dry_run
Logical; preview command without executing.
- echo
Logical; echo stdout/stderr in real time.