fsbrain (version 0.5.5)

write.group.morph.standard: Write standard space group data to a standard FreeSurfer directory stucture.

Description

Write standard space group data to a standard FreeSurfer directory stucture.

Usage

write.group.morph.standard(
  subjects_dir,
  subjects_list,
  data,
  measure_name,
  hemi = "both",
  fwhm = "10",
  template_subject = "fsaverage",
  format = "mgh",
  create_dirs = TRUE,
  template_lh_numverts = NULL
)

Arguments

subjects_dir

string. The FreeSurfer SUBJECTS_DIR, i.e., a directory containing the data for all your subjects, each in a subdir named after the subject identifier.

subjects_list

vector of strings. The subject identifiers.

data

the data matrix

measure_name

character string, the data part of the generated file names, e.g., 'thickness' or 'area'.

hemi

string, one of 'lh', 'rh' or 'both'. The hemisphere name. Used to construct the names of the annotation and morphometry data files to be loaded.

fwhm

string. Smoothing as string, e.g. '10' or '25'.

template_subject

string. Template subject name, defaults to 'fsaverage'.

format

string. One of 'mgh', 'mgz', 'curv'. Defaults to 'mgh'.

create_dirs

logical, whether to create missing (sub) directories which occur in the 'filepaths'.

template_lh_numverts

positive integer, the vertex count of the left hemi of the template subject, only used if 'hemi' is 'both'. If hemi is both and this is unspecified (left at the default value NULL), the template subject needs to exist in the 'subjects_dir' to determine the vertex count of the left hemisphere, so that the data can be split into the lh and rh files at the correct index.

See Also

write.group.morph.standard.sf and write.group.morph.standard.mf

Examples

if (FALSE) {
dm = matrix(rnorm(325684 * 6, 5.0, 1.2), ncol = 6);
subjects = paste("subject", seq(6), sep="");
write.group.morph.standard("/tmp/groupdata", subjects, dm,
  "rand", template_lh_numverts = 325684 / 2);
}