Uses FSL cluster to perform clustering on statistical output
Usage
ni_fsl_cluster(
in_file,
threshold,
args = NULL,
connectivity = NULL,
cope_file = NULL,
dlh = NULL,
find_min = FALSE,
fractional = FALSE,
minclustersize = FALSE,
no_table = FALSE,
num_maxima = NULL,
out_index_file = NULL,
out_localmax_txt_file = NULL,
out_localmax_vol_file = NULL,
out_max_file = NULL,
out_mean_file = NULL,
out_pval_file = NULL,
out_size_file = NULL,
out_threshold_file = NULL,
peak_distance = NULL,
pthreshold = NULL,
std_space_file = NULL,
use_mm = FALSE,
volume = NULL,
warpfield_file = NULL,
xfm_file = NULL,
.cwd = NULL,
.env = NULL,
.engine = NULL,
.profile = NULL,
dry_run = FALSE,
echo = interactive()
)Arguments
- in_file
Character; file path. input volume Required.
- threshold
Numeric. threshold for input volume Required.
- args
Character. Additional parameters to the command
- connectivity
Integer. the connectivity of voxels (default 26)
- cope_file
Character; file path. cope volume
- dlh
Numeric. smoothness estimate = sqrt(det(Lambda))
- find_min
Logical. find minima instead of maxima
- fractional
Logical. interprets the threshold as a fraction of the robust range
- minclustersize
Logical. prints out minimum significant cluster size
- no_table
Logical. suppresses printing of the table info
- num_maxima
Integer. no of local maxima to report
- out_index_file
Character or numeric vector. output of cluster index (in size order)
- out_localmax_txt_file
Character or numeric vector. local maxima text file
- out_localmax_vol_file
Character or numeric vector. output of local maxima volume
- out_max_file
Character or numeric vector. filename for output of max image
- out_mean_file
Character or numeric vector. filename for output of mean image
- out_pval_file
Character or numeric vector. filename for image output of log pvals
- out_size_file
Character or numeric vector. filename for output of size image
- out_threshold_file
Character or numeric vector. thresholded image
- peak_distance
Numeric. minimum distance between local maxima/minima, in mm (default 0)
- pthreshold
Numeric. p-threshold for clusters
- std_space_file
Character; file path. filename for standard-space volume
- use_mm
Logical. use mm, not voxel, coordinates
- volume
Integer. number of voxels in the mask
- warpfield_file
Character; file path. file containing warpfield
- xfm_file
Character; file path. filename for Linear: input->standard-space transform. Non-linear: input->highres transform
- .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.