ravecore (version 0.1.0)

cmd_run_dcm2niix: Convert DICOM to NIfTI via 'dcm2niix'

Description

Check https://rave.wiki on how to set up 'conda' environment for 'RAVE' using 'ravemanager'.

Usage

cmd_run_dcm2niix(
  subject,
  src_path,
  type = c("MRI", "CT"),
  merge = c("Auto", "No", "Yes"),
  float = c("Yes", "No"),
  crop = c("No", "Yes", "Ignore"),
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run
)

Value

A command set running the terminal command; a folder named with type will be created under the subject image input folder

Arguments

subject

'RAVE' subject or a subject ID

src_path

source directory

type

image type

merge, float, crop

'dcm2niix' parameters

overwrite

overwrite existing files

command_path

path to program 'dcm2niix'

dry_run

whether to dry-run

verbose

whether to print out command

Examples

if (FALSE) {

cmd_run_dcm2niix(
  "YAEL/pt02",
  "/path/to/DICOMDIR",
  "MRI"
)

}