fsbrain (version 1.0.0)

template.vol2surf: Project a volume onto a template surface like fsaverage or fs_LR_32.

Description

Samples a volume at the positions of the vertices of a template surface, e.g., for group-level statistical maps. The volume and the template surface must be defined in the same coordinate space: fsaverage is the FreeSurfer template and its surfaces are in MNI305 (surface RAS) space, while the fs_LR_32 template (the HCP-style 32k surface space) is in MNI152 space. Projecting an MNI152 volume onto fsaverage (or vice versa) will produce wrong results, but this function will usually detect it and warn (see check_fov).

This is the equivalent of the project_vol2surf function of the Python package yabplot for the fs_LR_32 template, and of mri_vol2surf for fsaverage. See subject.vol2surf for the per-subject variant, which uses the native space of a subject.

Usage

template.vol2surf(
  volume,
  template = "fsaverage",
  surface = NULL,
  hemi = "both",
  subjects_dir = NULL,
  surface_frac = NULL,
  frac_surface = "pial",
  interpolation = "trilinear",
  frame = 1L,
  cortex_only = FALSE,
  clamp = FALSE,
  check_fov = TRUE,
  affine = NULL,
  vox2ras = "auto"
)

Value

a numerical vector of per-vertex values, or a hemilist of such vectors if hemi is 'both'. See subject.vol2surf.

Arguments

volume

character string or named list, see subject.vol2surf. For template projections, this is typically the filepath of a NIfTI file containing a group-level map, e.g., in MNI152 space.

template

character string, the template identifier. One of 'fsaverage' (the FreeSurfer template, in MNI305 space) or 'fs_LR_32' (the HCP-style 32k template, in MNI152 space). Additional templates can be used by passing the respective subjects_dir and a template identifier that matches a directory in it.

surface

character string, the name of the surface to sample. Examples: 'white', 'pial', 'midthickness', 'inflated'. Defaults to 'white' for 'fsaverage' and to 'midthickness' for 'fs_LR_32' if surface is NULL.

hemi

character string, see subject.vol2surf.

subjects_dir

character string or NULL, the subjects dir which contains the template subject. If NULL (the default), the fsbrain data cache (see get_optional_data_filepath) is searched first, then the FreeSurfer installation. If the required files are missing, the respective download function is suggested in the error message.

surface_frac

numeric scalar or NULL, see subject.vol2surf.

frac_surface

character string, see subject.vol2surf.

interpolation

character string, see subject.vol2surf.

frame

positive integer scalar, see subject.vol2surf.

cortex_only

logical, see subject.vol2surf. For 'fsaverage', the required label/?h.cortex.label file is part of the FreeSurfer installation, for 'fs_LR_32' it can be downloaded with download_fs_LR_32_labels.

clamp

logical, see subject.vol2surf.

check_fov

logical, see subject.vol2surf.

affine

numeric 4x4 matrix or NULL, see subject.vol2surf.

vox2ras

character string, see subject.vol2surf.

See Also

Other volume to surface projection functions: subject.vol2surf()

Examples

if (FALSE) {
   # Project a group-level stat map (e.g., in MNI152 space) onto the HCP-style fs_LR_32 template:
   fsbrain::download_fs_LR_32_meshes();
   subjects_dir = fsbrain::get_optional_data_filepath("subjects_dir");
   stat_map = template.vol2surf("/path/to/your_statmap.nii.gz", template = "fs_LR_32",
       surface = "midthickness", subjects_dir = subjects_dir);
   # Project an MNI305 map onto fsaverage:
   stat_map = template.vol2surf("/path/to/your_mni305_map.nii.gz", template = "fsaverage",
       surface = "white");
}