Load FSL-distributed atlases into the standard neuroatlas `atlas` object shape. FSL atlases are described by XML files under `$FSLDIR/data/atlases`; many probabilistic atlases provide both a 4D probability image and a 3D maximum-probability summary image. The summary image labels are offset by one relative to XML/probability-volume indices, so `get_fsl_atlas()` applies that correction when loading max-probability summaries.
Usage
get_fsl_atlas(
name,
fsl_dir = Sys.getenv("FSLDIR"),
resolution = NULL,
image = c("summary", "probability"),
outspace = NULL,
path_only = FALSE
)Arguments
- name
Atlas identifier, FSL XML path, or known alias. Known aliases include `"harvard_oxford_cortical"`, `"harvard_oxford_subcortical"`, `"harvard_oxford_cortical_subcortical"`, and `"julich"`.
- fsl_dir
FSL installation directory. Defaults to `Sys.getenv("FSLDIR")`. `get_julich_brain_atlas()` downloads an FSL-style Julich-Brain cache when this is empty and `download = TRUE`.
- resolution
Preferred image resolution, e.g. `"1mm"` or `"2mm"`. If `NULL`, the first image entry in the XML file is used.
- image
One of `"summary"` or `"probability"`. `neuroatlas` atlas objects are discrete parcellations, so `"summary"` is the default. `"probability"` currently returns paths and metadata when `path_only = TRUE`; loading 4D probabilistic images as atlas objects is intentionally deferred.
- outspace
Optional `NeuroSpace` to resample the discrete atlas into.
- path_only
Logical; return resolved paths and parsed metadata without loading image data.