fsl_cluster: Form clusters, report information about clusters and/or...

In neuroconductor-releases/fslr: Wrapper Functions for 'FSL' ('FMRIB' Software Library) from Functional MRI of the Brain ('FMRIB')

Description

Form clusters, report information about clusters and/or perform cluster-based inference. Wrapper for cluster

Usage

fsl_cluster(
  file,
  threshold,
  retimg = FALSE,
  reorient = FALSE,
  opts = "",
  cope_image = NULL,
  pthresh = NULL,
  peakdist = 0,
  volume = FALSE,
  smooth_est = NULL,
  voxel_resel = NULL,
  fractional = FALSE,
  connectivity = 26,
  mm = FALSE,
  find_minima = FALSE,
  standard_image = NULL,
  verbose = TRUE,
  ...
)

fslcluster(..., retimg = TRUE)

read_cluster_table(file)

Arguments

file	filename of input volume
threshold	threshold for input volume
retimg	(logical) return image of class nifti
reorient	(logical) If retimg, should file be reoriented when read in? Passed to readnii.
opts	(character) operations to be passed to cluster
cope_image	filename of input cope volume
pthresh	p-threshold
peakdist	minimum distance between local maxima/minima, in mm (default 0)
volume	number of voxels in the mask
smooth_est	smoothness estimate = sqrt(det(Lambda))
voxel_resel	Size of one resel in voxel units
fractional	interprets the threshold as a fraction of the robust range
connectivity	the connectivity of voxels (default 26)
mm	use mm, not voxel, coordinates
find_minima	find minima instead of maxima
standard_image	filename for standard-space volume
verbose	(logical) print out command before running
...	additional arguments to pass to fslcmd

Value

A list of filenames of outputs and tables:

• opvalsfilename for image output of log pvals

• oindexfilename for output of cluster index (in size order)

• othreshfilename for output of thresholded image

• olmaxfilename for output of local maxima text file

• olmaximfilename for output of local maxima volume

• osizefilename for output of size image

• omaxfilename for output of max image

• omeanfilename for output of mean image

Examples

if (have_fsl()) { 
file = mni_fname(brain = TRUE, mask = FALSE)
threshold = 6000
clus = fsl_cluster(file, threshold)
}

neuroconductor-releases/fslr documentation built on Nov. 14, 2020, 11:55 p.m.