qdecr_fastlm: Vertex-wise linear regression
In slamballais/QDECR: Vertex-wise statistical analysis

Vertex-wise linear regression

qdecr_fastlm(
  formula,
  data,
  id,
  hemi,
  weights = NULL,
  dir_out = getwd(),
  project,
  n_cores = 1,
  target = "fsaverage",
  fwhm = ifelse(measure == "pial_lgi", 5, 10),
  mcz_thr = 0.001,
  cwp_thr = 0.025,
  mgh = NULL,
  mask = NULL,
  mask_path = system.file("extdata", paste0(hemi, ".fsaverage.cortex.mask.mgh"),
    package = "QDECR"),
  dir_subj = Sys.getenv("SUBJECTS_DIR"),
  dir_fshome = Sys.getenv("FREESURFER_HOME"),
  dir_tmp = dir_out,
  dir_out_tree = TRUE,
  file_out_tree = !dir_out_tree,
  clean_up_bm = TRUE,
  clean_up = TRUE,
  clobber = FALSE,
  verbose = TRUE,
  save = TRUE,
  save_data = TRUE,
  debug = FALSE,
  custom_measure = NULL,
  prep_fun = "prep_fastlm",
  analysis_fun = "analysis_chunkedlm",
  chunk_size = 1000
)

`formula`	an object of class "formula" (or one that can be coerced to that class): a symbolic description of the model to be fitted. See '?lm'.
`data`	a required argument that contains a data frame, a list of data frames or an imputed object that is supported by the 'imp2list' function (mice, mi, etc.).
`id`	the name of the id variable that matches the dataset to the Freesurfer output
`hemi`	hemisphere to analyze ("lh" or "rh")
`weights`	Optinal vector of weights for the observations. See '?lm'.
`dir_out`	the directory where to save the data to (defaults to the current directory)
`project`	the base name you want to assign to the output files
`n_cores`	the number of cores to be used
`target`	the target template (default = "fsaverage")
`fwhm`	full width half max (default = 10 mm, for pial_lgi it is 5 mm)
`mcz_thr`	A numeric value for the Monte Carlo simulation threshold (default: 0.001). 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, 33/3.3/0.0005, 40/4.0/0.0001.
`cwp_thr`	the cluster-wise p-value threshold on top of all correction (default = 0.025, as there are 2 hemispheres)
`mgh`	NOT IMPLEMENTED; path to existing merged mgh file, default is NULL
`mask`	mgh file to mask analysis; default is to use the cortex label from the target
`mask_path`	path to the mask; default is the cortex mask that is provided with the QDECR package
`dir_subj`	directory contain the surface-based maps (mgh files); defaults to SUBJECTS_DIR
`dir_fshome`	Freesurfer directory; defaults to FREESURFER_HOME
`dir_tmp`	directory to store the temporary big matrices; useful for shared memory; defaults to 'dir_out'
`dir_out_tree`	if TRUE, creates a dir_out/project directory. If FALSE, all output is placed directory into dir_out
`file_out_tree`	if TRUE, adds the full project name to the output file names. By default it is the inverse of dir_out_tree
`clean_up_bm`	if TRUE, cleans all big matrices (.bk) that were generated in dir_tmp
`clean_up`	NOT IMPLEMENTED; will be used for setting cleaning of other files
`clobber`	if TRUE, ignores already existing directories and writes over them; if FALSE, stops and warns user that a given directory already exists
`verbose`	if TRUE, writes out standard log; if FALSE, no output is generated
`save`	if TRUE, saves the output to a .rds file
`save_data`	if TRUE, includes the raw data + design matrices in the .rds file
`debug`	NOT IMPLEMENTED; will output the maximal log to allow for easy debugging
`custom_measure`	a string that starts with "qdecr_" followed by the name of a surface file that is not created by FreeSurfer by default (e.g. "qdecr_cc" or "qdecr_test"). Note that the surface files MUST be located in the surf subdirectory of each individual's FreeSurfer output, and the files must follow the naming conventions of the other .mgh files (e.g. "lh.test.fwhm10.fsaverage.mgh")
`prep_fun`	Name of the function that needs to be called for the preparation step (do not touch unless you know what you are doing!)
`analysis_fun`	Name of the function that needs to be called for the analysis step (do not touch unless you know what you are doing!)
`chunk_size`	Integer; the desired chunk size for the chunked lm