oasisad_df: OASIS Data Frame

In dty0606/oasisad: 'OASISAD' an Improved Automated White Matter Hyper-intensity Classficiation Tool

Description

This function creates data frame for OASIS models

Usage

oasisad_df(
  flair,
  t1,
  t2 = NULL,
  pd = NULL,
  gold_standard = NULL,
  preproc = TRUE,
  brain_mask = NULL,
  img_space = FALSE,
  neighbor = TRUE,
  wm_mask = NULL,
  seg_mask = NULL,
  dir = NULL,
  eroder = TRUE,
  voxel_select = NULL,
  normalize = TRUE,
  image_sm = TRUE,
  slices = NULL,
  orientation = c("axial", "coronal", "sagittal"),
  return_pre = FALSE,
  cores = 1,
  verbose = TRUE
)

Arguments

flair	Input FLAIR image
t1	Input T1 image
t2	Input T2 image
pd	Input PD image
gold_standard	gold standard lesion segmentation mask of class nifti
preproc	A boolean indicates whether to call oasisad_pre function or not
brain_mask	Input brain_mask, if null, a mask will be obtained by FSL
img_space	An image to register, if NULL, 'flair' image will be used in registration.
neighbor	A boolean indicates whether will use neighbor refinement function in model step. If true, either prepare segmentation and white matter mask to input in this function or this functoin will generate masks by fslr
wm_mask	Input of white matter mask
seg_mask	Input of segmentation mask
dir	A user defined output path for fslr segmentation
eroder	A boolean indicates whether should use fslerode
voxel_select	A specifed level to remove voxels whose intensity under
normalize	A boolean indicates whether to perform z-score normalization of the image over the brain mask, should be TRUE unless you train model using an alternative normalization. Normoalization is a recommended step in image preprocessing.
image_sm	A boolean indates whether to smooth images and used as predictors in model
slices	vector of desired slices to train on, if NULL then train over the entire brain mask
orientation	string value telling which orientation the training slices are specified in, can take the values of "axial", "sagittal", or "coronal"
return_pre	is a logical value that indicates whether the preprocessed images should be returned
cores	numeric indicating the number of cores to be used
verbose	A boolean indicated whether output messages

Value

OASISAS data structure

dty0606/oasisad documentation built on March 8, 2020, 11:18 p.m.