Run a built-in 'YAEL' imaging processing workflow

Image processing pipeline doi:10.1523/ENEURO.0328-23.2023 , allowing cross-modality image registration, 'T1'-weighted 'MRI' normalization to template brain, creating subject-level brain atlas from inverse normalization.

Usage

yael_preprocess(
  subject,
  t1w_path = NULL,
  ct_path = NULL,
  t2w_path = NULL,
  fgatir_path = NULL,
  preopct_path = NULL,
  flair_path = NULL,
  t1w_contrast_path = NULL,
  register_policy = c("auto", "all"),
  register_reversed = FALSE,
  normalize_template = "mni_icbm152_nlin_asym_09b",
  normalize_policy = c("auto", "all"),
  normalize_images = c("T1w", "T2w", "T1wContrast", "fGATIR", "preopCT"),
  normalize_back = ifelse(length(normalize_template) >= 1, normalize_template[[1]], NA),
  atlases = list(),
  add_surfaces = FALSE,
  verbose = TRUE,
  ...
)

cmd_run_yael_preprocess(
  subject,
  t1w_path = NULL,
  ct_path = NULL,
  t2w_path = NULL,
  fgatir_path = NULL,
  preopct_path = NULL,
  flair_path = NULL,
  t1w_contrast_path = NULL,
  register_reversed = FALSE,
  normalize_template = "mni_icbm152_nlin_asym_09b",
  normalize_images = c("T1w", "T2w", "T1wContrast", "fGATIR", "preopCT"),
  run_recon_all = TRUE,
  dry_run = FALSE,
  verbose = TRUE,
  ...
)

Arguments

subject

subject ID

t1w_path

path to 'T1'-weighted preoperative 'MRI', used as underlay and base image. If you want to have 'ACPC' aligned scanner coordinate system. Please align the image before feeding into this function. All images must contain skulls (do not strip skulls)

ct_path, t2w_path, fgatir_path, preopct_path, flair_path, t1w_contrast_path

additional optional images to be aligned to the underlay; the registration will be symmetric and the rigid-body transforms will be stored.

register_policy

whether to skip already registered images; default is true ('auto'); set to 'all' to ignore existing registrations and force calculation

register_reversed

whether to swap the moving images and the fixing image; default is false

normalize_template

template to normalize to: default is 'mni_icbm152_nlin_asym_09b' ('MNI152b', 0.5 mm resolution); when the computer memory is below 12 gigabytes, the template will automatically switch to 'mni_icbm152_nlin_asym_09a' (known as 'MNI152a', 1 mm voxel resolution). Other choices are 'mni_icbm152_nlin_asym_09c' and 'fsaverage' (or known as 'MNI305')

normalize_policy

whether to skip existing normalization, if calculated; default is 'auto' (yes); set to 'all' to ignore

normalize_images

images used for normalization; default is to include common images before the implantation (if available)

normalize_back

length of one (select from normalize_template), which template is to be used to generate native brain mask and transform matrices

atlases

a named list: the names must be template names from normalize_template and the values must be directories of atlases of the corresponding templates (see 'Examples').

add_surfaces

whether to add surfaces for the subject; default is FALSE. The surfaces are created by reversing the normalization from template brain, hence the results will not be accurate. Enable this option only if cortical surface estimation is not critical (and 'FreeSurfer' reconstructions are inaccessible)

verbose

whether to print out the information; default is TRUE

...

reserved for legacy code and deprecated arguments

run_recon_all

whether to run 'FreeSurfer'; default is true

dry_run

whether to dry-run

Value

Nothing, a subject imaging folder will be created under 'RAVE' raw folder. It will take a while to run the workflow.

Examples

if (FALSE) { # \dontrun{

# For T1 normalization only; add ct_path to include coregistration
cmd_run_yael_preprocess(
  subject = "pt01",
  t1w_path = "/path/to/T1w.nii.gz",

  # normalize T1 to MNI152
  normalize_template = 'mni_icbm152_nlin_asym_09b'
)


} # }