vol_coords_to_fsaverage: Map MNI152 or Colin27 volume coords to fsaverage coords and...

In dfsp-spirit/regfusionr: Registration Fusion in R

Map MNI152 or Colin27 volume coords to fsaverage coords and vertices.

Description

Map MNI152 or Colin27 volume coords to fsaverage coords and vertices.

Usage

vol_coords_to_fsaverage(
  coords,
  surface = "white",
  fs_home = Sys.getenv("FS_HOME"),
  silent = TRUE,
  rf_type = "RF_ANTs",
  template_type = "FSL_MNI152"
)

Arguments

coords	nx3 numeric matrix, the source RAS coordinates in the input image which must be in MNI152/Colin27 space. The coords must be within the cortex, otherwise the mapping makes no sense and NaN values are returned for the respective coords.
surface	character string, the fsaverage surface (brain mesh) to load. Must be a valid FreeSurfer surface name like 'white', 'pial', 'orig, 'inflated'.
fs_home	character string, path to the FreeSurfer installation. Alternatively, a hemilist of freesurferformats::fs.surface instances like surface = list("lh"=mysurflh, "rh"=mysurfrh). Used to find the surfaces, at <fs_home>/subjects/fsaverage/surf/<hemi>.<surface>, where hemi is 'lh' and 'rh'. Can be NULL if 'surface' is a hemilist of fs.surface instances.
silent	logical, whether to suppress output messages in case of coords outside of cortex.
rf_type	the regfusion type to use, one of 'RF_ANTs' or 'RF_M3Z'.
template_type	character string, the source template or the space that your input image is in. One of 'MNI152_orig', 'Colin27_orig', 'MNI152_norm', 'Colin27_norm'.

Value

named list with entries 'fsaverage_vertices': integer vector of fsaverage surface vertex indices, 'hemi': vector of hemi strings for the vertices, 'fsaverage_coords': nx3 numeric matrix of target coordinates, 'query_mni_coords': copy of input parameter coords, 'query_mni_voxels': the voxel indices at the query RAS coords.

Author(s)

Tim Schäfer for the R version, Wu Jianxiao and CBIG for the original Matlab version.

Examples

## Not run: 
  mni_ras = c(60.0, 0.0, 10.0)
  res = vol_coords_to_fsaverage(mni_ras, surface = "white");
  res$fsaverage_vertices;   # 9092

## End(Not run)

dfsp-spirit/regfusionr documentation built on Sept. 4, 2022, 9:32 a.m.