fsaverage_to_vol: Project or map per-vertex values from the fsaverage surface...

In dfsp-spirit/regfusionr: Registration Fusion in R

Project or map per-vertex values from the fsaverage surface to the cortex voxels of an MNI volume.

Description

Applies the Wu et al. regfusion method to obtain MNI volume coordinates, then interpolates values.

Usage

fsaverage_to_vol(
  lh_input,
  rh_input,
  target_space = "FSL_MNI152",
  rf_type = "RF_ANTs",
  interp = "linear",
  out_type = "mgz",
  out_dir = NULL,
  fsaverage_path = NULL
)

Arguments

lh_input	numerical vector of per-vertex data for the left hemisphere of the template subject. Must contain 163842 values for the fsaverage template. Input for fsaverage6 (40962 values) or fsaverage5 (10242 values) can also be used and will be upsampled using nn_interpolate_kdtree. Automatic upsamping is only supported with interp='linear'.
rh_input	numerical vector of per-vertex data for the right hemisphere of the template subject. Must contain 163842 values for the fsaverage template. See description for lh_input for more details.
target_space	character string, the target template or the space that your output volume should be in. One of 'FSL_MNI152' or 'SPM_Colin27'.
rf_type	the regfusion type to use, one of 'RF_ANTs' or 'RF_M3Z'.
interp	interpolation method, currently only 'linear' and 'nearest' are supported. The performance of the 'linear' method is currently quite bad, and it will be rewritten in C++ when I find the time.
out_type	character string, the format of the output files. One of the following: 'mgz' or 'mgh' for FreeSurfer MGZ/MGH format, 'nii' for NIFTI v1 format. Ignored unless out_dir is not NULL.
out_dir	optional character string, the path to a writable output directory to which the output should be written as volume files. If NULL, no data is written to files. If out_dir is not NULL, the return value additionally contains the following keys: 'out_file' and the output file format at key 'out_format', (and 'out_file_seg'/'out_format_seg' for the respective seg versions).
fsaverage_path	character string or NULL, the file system path to the fsaverage directory (NOT including the 'fsaverage' dir itself). If NULL, defaults to the return value of fsbrain::fsaverage.path() on the system. This path is used to read the spherical surface (both hemisphere meshes) of the template subject.

Value

named list with keys 'projected' and 'projected_seg', each of which holds an fs.volume instance, its 'data' key holds a 256x256x256 array with the projected data. The data in 'projected_seg' is identical to the data in 'projected', with the exception that data values originating from the right hemisphere have been incremented by 1000. See out_dir parameter to easily write results to files. If out_dir is not NULL, the return value additionally contains the following keys: 'out_file' and the output file format at key 'out_format'.

Note

This function requires the packages 'fsbrain' and 'haze', which are optional dependencies. The package 'fsbrain' can be installed from CRAN. For 'haze', see https://github.com/dfsp-spirit/haze.

This function is quite expensive computationally, especially when using interp = 'linear'.

Author(s)

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

Examples

## Not run: 
  lh_input = rnorm(163842L, 3.0, 0.2);
  rh_input = rnorm(163842L, 3.0, 0.2);
  res = fsaverage_to_vol(lh_input, rh_input, "FSL_MNI152");

## End(Not run)

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