This function is a wrapper for the FreeSurfer command mri_surfcluster.
It computes the clusters of significant vertices.
Usage
compute_clusters(
stack_path,
hemi,
fwhm,
FS_HOME,
cwp_thr = 0.025,
mcz_thr = 30,
csd_sign = "abs",
full_surfcluster_output = FALSE,
mask = NULL,
verbose = FALSE
)Arguments
- stack_path
: path where this term's p values are stored and where results are generated.
- hemi
: hemisphere.
- fwhm
: full-width half maximum estimate of data smoothness.
- FS_HOME
: FreeSurfer directory, i.e.
$FREESURFER_HOME- cwp_thr
: (default = 0.025, when both hemispheres are ran, else 0.05) the cluster-wise p-value threshold on top of all corrections.
- mcz_thr
: (default = 0.001) numeric value for the Monte Carlo simulation threshold. Any of the following are accepted (equivalent values separate by `/`): * 13 / 1.3 / 0.05, * 20 / 2.0 / 0.01, . * 23 / 2.3 / 0.005, * 30 / 3.0 / 0.001, \* default * 33 / 3.3 / 0.0005, * 40 / 4.0 / 0.0001.
- csd_sign
: (default = "abs")
- full_surfcluster_output
: (default = FALSE) whether to save additional files:
.cluster.mgh: a map of cluster-wise significances files:.voxel.mgh: a map of corrected voxel-wise significance files:.ocn.annot: output clusters as an annotation files:.masked.mgh: input with non-clusters set to 0- mask
: apply a mask (default = cortical mask + excluding problematic vertices)
- verbose
: (default = FALSE) verbosity.