yael_preprocess: Process brain images for "YAEL"

In beauchamplab/raveio: File-System Toolbox for RAVE Project

Process brain images for 'YAEL'

Description

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 = "mni_icbm152_nlin_asym_09b",
  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

## Not run: 


# 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"
  )

)



## End(Not run)

beauchamplab/raveio documentation built on March 5, 2025, 11:06 p.m.