Multivariate Exploratory Linear Optimised Decomposition into Independent
Usage
ni_fsl_melodic(
in_files,
ICs = NULL,
approach = NULL,
args = NULL,
bg_image = NULL,
bg_threshold = NULL,
cov_weight = NULL,
dim = NULL,
dim_est = NULL,
epsilon = NULL,
epsilonS = NULL,
log_power = NULL,
mask = NULL,
max_restart = NULL,
maxit = NULL,
migp = NULL,
migpN = NULL,
migp_factor = NULL,
migp_shuffle = NULL,
mix = NULL,
mm_thresh = NULL,
no_bet = NULL,
no_mask = NULL,
no_mm = NULL,
non_linearity = NULL,
num_ICs = NULL,
out_all = NULL,
out_dir = NULL,
out_mean = NULL,
out_orig = NULL,
out_pca = NULL,
out_stats = NULL,
out_unmix = NULL,
out_white = NULL,
pbsc = NULL,
rem_cmp = NULL,
remove_deriv = NULL,
report = NULL,
report_maps = NULL,
s_con = NULL,
s_des = NULL,
sep_vn = NULL,
sep_whiten = NULL,
smode = NULL,
t_con = NULL,
t_des = NULL,
tr_sec = NULL,
update_mask = NULL,
var_norm = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_files
Character or numeric vector. input file names (either single file name or a list) Required.
- ICs
Character; file path. filename of the IC components file for mixture modelling
- approach
Character. approach for decomposition, 2D: defl, symm (default), 3D: tica (default), concat
- args
Character. Additional parameters to the command
- bg_image
Character; file path. specify background image for report (default: mean image)
- bg_threshold
Numeric. brain/non-brain threshold used to mask non-brain voxels, as a percentage (only if –nobet selected)
- cov_weight
Numeric. voxel-wise weights for the covariance matrix (e.g. segmentation information)
- dim
Integer. dimensionality reduction into #num dimensions (default: automatic estimation)
- dim_est
Character. use specific dim. estimation technique: lap, bic, mdl, aic, mean (default: lap)
- epsilon
Numeric. minimum error change
- epsilonS
Numeric. minimum error change for rank-1 approximation in TICA
- log_power
Logical. calculate log of power for frequency spectrum
- mask
Character; file path. file name of mask for thresholding
- max_restart
Integer. maximum number of restarts
- maxit
Integer. maximum number of iterations before restart
- migp
Logical. switch on MIGP data reduction
- migpN
Integer. number of internal Eigenmaps
- migp_factor
Integer. Internal Factor of mem-threshold relative to number of Eigenmaps (default: 2)
- migp_shuffle
Logical. randomise MIGP file order (default: TRUE)
- mix
Character; file path. mixing matrix for mixture modelling / filtering
- mm_thresh
Numeric. threshold for Mixture Model based inference
- no_bet
Logical. switch off BET
- no_mask
Logical. switch off masking
- no_mm
Logical. switch off mixture modelling on IC maps
- non_linearity
Character. nonlinearity: gauss, tanh, pow3, pow4
- num_ICs
Integer. number of IC's to extract (for deflation approach)
- out_all
Logical. output everything
- out_dir
Character; directory path. output directory name
- out_mean
Logical. output mean volume
- out_orig
Logical. output the original ICs
- out_pca
Logical. output PCA results
- out_stats
Logical. output thresholded maps and probability maps
- out_unmix
Logical. output unmixing matrix
- out_white
Logical. output whitening/dewhitening matrices
- pbsc
Logical. switch off conversion to percent BOLD signal change
- rem_cmp
Character or numeric vector. component numbers to remove
- remove_deriv
Logical. removes every second entry in paradigm file (EV derivatives)
- report
Logical. generate Melodic web report
- report_maps
Character. control string for spatial map images (see slicer)
- s_con
Character; file path. t-contrast matrix across subject-domain
- s_des
Character; file path. design matrix across subject-domain
- sep_vn
Logical. switch off joined variance normalization
- sep_whiten
Logical. switch on separate whitening
- smode
Character; file path. matrix of session modes for report generation
- t_con
Character; file path. t-contrast matrix across time-domain
- t_des
Character; file path. design matrix across time-domain
- tr_sec
Numeric. TR in seconds
- update_mask
Logical. switch off mask updating
- var_norm
Logical. switch off variance normalization
- .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.