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Process brain images for 'YAEL'

Source: R/cmd-recon-all.R, R/image-preprocess.R
yael_preprocess.Rd

Aligns 'T1w' with other image types; normalizes 'T1w' 'MRI' to 'MNI152' templates via symmetric non-linear morphs. Create brain custom atlases from templates.

Usage

cmd_run_yael_preprocess(
  subject_code,
  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 = c("mni_icbm152_nlin_asym_09a", "mni_icbm152_nlin_asym_09c"),
  run_recon_all = TRUE,
  dry_run = FALSE,
  verbose = TRUE
)

yael_preprocess(
  subject_code,
  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_09a",
  normalize_policy = c("auto", "all"),
  normalize_back = ifelse(length(normalize_template) >= 1, normalize_template[[1]], NA),
  atlases = list(),
  add_surfaces = FALSE,
  verbose = TRUE
)

Arguments

subject_code

'RAVE' subject code

t1w_path

(required) 'T1' weighted 'MRI' path

ct_path

(optional in general but mandatory for electrode localization) post-surgery 'CT' path

t2w_path

(optional) 'T2' weighted 'MRI' path

fgatir_path

(optional) 'fGATIR' (fast gray-matter acquisition 'T1' inversion recovery) image path

preopct_path

(optional) pre-surgery 'CT' path

flair_path

(optional) 'FLAIR' (fluid-attenuated inversion recovery) image path

t1w_contrast_path

(optional) 'T1' weighted 'MRI' with contrast (usually used to show the blood vessels)

register_reversed

direction of the registration; FALSE (default) registers other images (such as post-surgery 'CT' to 'T1'); set to FALSE if you would like the 'T1' to be registered into other images. Since 'YAEL' does not re-sample the images, there is no essential difference on the final registration results

normalize_template

names of the templates which the native 'T1' images will be normalized into

run_recon_all

whether to run 'FreeSurfer' reconstruction; default is true

dry_run

whether to dry-run the script and check if error exists before actually execute the scripts.

verbose

whether to print out the progress; default is TRUE

register_policy

whether images should be registered with 'T1w' image; default is "auto": automatically run registration algorithm if missing; alternative is "all": force the registration algorithm even if mapping files exist

normalize_policy

normalization policy; similar to register_policy but is applied to normalization. Default is "auto": automatically run normalization when the mapping is missing, and skip if exists; alternative is "all": force to run the normalization.

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.

Value

Nothing, a subject imaging folder will be created under 'RAVE' raw folder

Examples


if (FALSE) { # \dontrun{


# For T1 preprocessing only
yael_preprocess(
  subject_code = "patient01",
  t1w_path = "/path/to/T1.nii or T1.nii.gz",

  # normalize T1 to all 2009 MNI152-Asym brains (a,b,c)
  normalize_template = c(
    "mni_icbm152_nlin_asym_09a",
    "mni_icbm152_nlin_asym_09b",
    "mni_icbm152_nlin_asym_09c"
  ),

  # only normalize if not exists
  normalize_policy = "auto",

  # use MNI152b to create native processing folder
  normalize_back = "mni_icbm152_nlin_asym_09b",

  # Atlases generated from different templates have different
  # coordinates, hence both folder path and template names must be
  # provided
  atlases = list(
    mni_icbm152_nlin_asym_09b = "/path/to/atlas/folder1",
    mni_icbm152_nlin_asym_09c = "/path/to/atlas/folder2"
  )

)

# For T1 and postop CT coregistration only
yael_preprocess(
  subject_code = "patient01",
  t1w_path = "/path/to/T1.nii or T1.nii.gz",
  ct_path = "/path/to/CT.nii or CT.nii.gz",

  # No normalization
  normalize_template = NULL,
  normalize_back = NA

)

# For both T1 and postop CT coregistration and T1 normalization
yael_preprocess(
  subject_code = "patient01",
  t1w_path = "/path/to/T1.nii or T1.nii.gz",
  ct_path = "/path/to/CT.nii or CT.nii.gz",

  normalize_template = c(
    "mni_icbm152_nlin_asym_09a",
    "mni_icbm152_nlin_asym_09b",
    "mni_icbm152_nlin_asym_09c"
  ),

  normalize_policy = "auto",

  normalize_back = "mni_icbm152_nlin_asym_09b",

  atlases = list(
    mni_icbm152_nlin_asym_09b = "/path/to/atlas/folder1",
    mni_icbm152_nlin_asym_09c = "/path/to/atlas/folder2"
  )

)


} # }