fsbrain (version 0.4.2)

subject.volume: Read a brain volume.

Description

Load a brain volume (like `mri/brain.mgz`) for a subject from disk. Uses knowledge about the FreeSurfer directory structure to load the correct file.

Usage

subject.volume(
  subjects_dir,
  subject_id,
  volume,
  format = "auto",
  drop_empty_dims = TRUE,
  with_header = FALSE,
  mri_subdir = NULL
)

Arguments

subjects_dir

character string, the FreeSurfer `SUBJECTS_DIR`, i.e., a directory containing the data for all your subjects, each in a subdir named after the subject identifier.

subject_id

character string, the subject identifier.

volume

character string, name of the volume file without file extension. Examples: `brain` or `aseg`.

format

string. One of 'mgh', 'mgz', 'AUTO'. If left at the default value 'AUTO', the function will look for files with extensions 'mgh' and 'mgz' (in that order) and use the first one that exists.

drop_empty_dims

logical, whether to drop empty dimensions of the returned data. Passed to read.fs.mgh.

with_header

logical. Whether to return the header as well. If TRUE, return a named list with entries "data" and "header". The latter is another named list which contains the header data. These header entries exist: "dtype": int, one of: 0=MRI_UCHAR; 1=MRI_INT; 3=MRI_FLOAT; 4=MRI_SHORT. "voldim": integer vector. The volume (=data) dimensions. E.g., c(256, 256, 256, 1). These header entries may exist: "vox2ras_matrix" (exists if "ras_good_flag" is 1), "mr_params" (exists if "has_mr_params" is 1). Passed to read.fs.mgh.

mri_subdir

character string or NULL, the subdir to use within the `mri` directory. Defaults to `NULL`, which means to read directly from the `mri` dir. You could use this to read volumes from the `mri/orig/` directory by setting it to `orig`.

Value

numerical array, the voxel data. If `with_header`, the full volume datastructure (see above).

Examples

# NOT RUN {
   fsbrain::download_optional_data();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   brain = subject.volume(subjects_dir, 'subject1', 'brain', with_header = TRUE);
   # Use the vox2ras matrix from the header to compute RAS coordinates at CRS voxel (0, 0, 0):
   brain$header$vox2ras_matrix %*% c(0,0,0,1);
# }
# NOT RUN {
# }