qdecr

Usage

qdecr(
  id,
  data,
  vertex = "qdecr",
  margs = NULL,
  model = c("stats::lm", "QDECR::megha", "RcppEigen::fastLm", "stats::glm",
    "survival::coxph", "default"),
  target = "fsaverage",
  hemi = c("lh", "rh"),
  measure = c("thickness", "area", "area.pial", "curv", "jacobian_white", "pial",
    "pial_lgi", "sulc", "volume", "w_g.pct", "white.H", "white.K"),
  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"),
  project,
  dir_subj = Sys.getenv("SUBJECTS_DIR"),
  dir_fshome = Sys.getenv("FREESURFER_HOME"),
  dir_tmp = dir_out,
  dir_out,
  dir_out_tree = TRUE,
  file_out_tree = !dir_out_tree,
  clean_up = TRUE,
  clean_up_bm = TRUE,
  clobber = FALSE,
  verbose = TRUE,
  debug = FALSE,
  n_cores = 1,
  prep_fun = "prep_fastlm",
  analysis_fun = "analysis_chunkedlm",
  chunk_size = 1000
)

Arguments

id

the name of the id variable that matches the dataset to the Freesurfer output

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.).

vertex

the preposition to the vertex measure (default: "qdecr_")

margs

the arguments that should be provided to the function of interest (e.g. stats::lm)

model

the function to grab the arguments from (this will be removed in a later version)

target

the target template (default = "fsaverage")

hemi

hemisphere to analyze ("lh" or "rh")

measure

the vertex-wise measure to use ("thickness", "area", etc.)

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

project

the base name you want to assign to the output files

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

the directory where to save the data to (defaults to the current directory)

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

NOT IMPLEMENTED; will be used for setting cleaning of other files

clean_up_bm

if TRUE, cleans all big matrices (.bk) that were generated in dir_tmp

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

debug

NOT IMPLEMENTED; will output the maximal log to allow for easy debugging

n_cores

the number of cores to be used

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

Value

Details