External shell commands for 'RAVE' — cmd_run

These shell commands are for importing 'DICOM' images to 'Nifti' format, reconstructing cortical surfaces, and align' the CT' to 'MRI'. The commands are only tested on 'MacOS' and 'Linux'. On 'Windows' machines, please use the 'WSL2' system.

Usage

cmd_run_3dAllineate(
  subject,
  mri_path,
  ct_path,
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run
)

cmd_execute(
  script,
  script_path,
  command = "bash",
  dry_run = FALSE,
  backup = TRUE,
  args = NULL,
  ...
)

cmd_run_r(
  expr,
  quoted = FALSE,
  verbose = TRUE,
  dry_run = FALSE,
  log_file = tempfile(),
  script_path = tempfile(),
  ...
)

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
)

cmd_run_flirt(
  subject,
  mri_path,
  ct_path,
  dof = 6,
  cost = c("mutualinfo", "leastsq", "normcorr", "corratio", "normmi", "labeldiff", "bbr"),
  search = 90,
  searchcost = c("mutualinfo", "leastsq", "normcorr", "corratio", "normmi", "labeldiff",
    "bbr"),
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run
)

cmd_run_recon_all(
  subject,
  mri_path,
  args = c("-all", "-autorecon1", "-autorecon2", "-autorecon3", "-autorecon2-cp",
    "-autorecon2-wm", "-autorecon2-pial"),
  work_path = NULL,
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run
)

cmd_run_recon_all_clinical(
  subject,
  mri_path,
  work_path = NULL,
  overwrite = FALSE,
  command_path = NULL,
  dry_run = FALSE,
  verbose = dry_run,
  ...
)

Arguments

subject: characters or a RAVESubject instance
mri_path: the absolute to 'MRI' volume; must in 'Nifti' format
ct_path: the absolute to 'CT' volume; must in 'Nifti' format
overwrite: whether to overwrite existing files; default is false
command_path: command line path if 'RAVE' cannot find the command binary files
dry_run: whether to run in dry-run mode; under such mode, the shell command will not execute. This is useful for debugging scripts; default is false
verbose: whether to print out the command script; default is true under dry-run mode, and false otherwise
script: the shell script
script_path: path to run the script
command: which command to invoke; default is 'bash'
backup: whether to back up the script file immediately; default is true
args: further arguments in the shell command, especially the 'FreeSurfer' reconstruction command
...: passed to system2, or additional arguments
expr: expression to run as command
quoted: whether expr is quoted; default is false
log_file: where should log file be stored
src_path: source of the 'DICOM' or 'Nifti' image (absolute path)
type: type of the 'DICOM' or 'Nifti' image; choices are 'MRI' and 'CT'
merge, float, crop: 'dcm2niix' conversion arguments; ignored when the source is in 'Nifti' format
dof, cost, search, searchcost: parameters used by 'FSL' 'flirt' command; see their documentation for details
work_path: work path for 'FreeSurfer' command;

Value

A list of data containing the script details:

script: script details
script_path: where the script should/will be saved
dry_run: whether dry-run mode is turned on
log_file: path to the log file
execute: a function to execute the script