Read `FreeSurfer` surface and volume files

Read `FreeSurfer` surface and volume files

Usage

freesurfer_brain(
  fs_subject_folder,
  subject_name,
  additional_surfaces = NULL,
  aligned_ct = NULL,
  use_cache = TRUE,
  use_141 = getOption("threeBrain.use141", TRUE)
)

freesurfer_brain2(
  fs_subject_folder,
  subject_name,
  volume_types = "t1",
  surface_types = "pial",
  curvature = "sulc",
  atlas_types = c("aparc+aseg", "aparc.a2009s+aseg", "aparc.DKTatlas+aseg"),
  ct_path = NULL,
  use_cache = TRUE,
  use_141 = getOption("threeBrain.use141", TRUE),
  ...
)

Arguments

fs_subject_folder

character, `FreeSurfer` subject folder, or `RAVE` subject folder

subject_name

character, subject code to display with only letters and digits

additional_surfaces

character array, additional surface types to load, such as `white`, `smoothwm`

aligned_ct

character, path to `ct_aligned_mri.nii.gz`, used for electrode localization

use_cache

logical, whether to use cached `json` files or from raw `FreeSurfer` files

use_141

logical, whether to use standard 141 brain for surface file, default is getOption('threeBrain.use141', TRUE)

volume_types

volume types, right now only support T1 image

surface_types

surface types to load

curvature

curvature data. Only support "sulc" for current version

atlas_types

atlas types to be loaded, choices are 'aparc+aseg', 'aparc.a2009s+aseg', 'aparc.DKTatlas+aseg', 'aseg'

ct_path

an aligned CT file in 'Nifti' format

...

ignored

Details

This function is under FreeSurfer license. 1. Volumes: 3D viewer uses `mri/T1.mgz` from `FreeSurfer` to show the volume information. `T1.mgz` results from step 1 to 5 in `FreeSurfer` command `recon-all -autorecon1`, which aligns the original `DICOM` image to `RAS` coordinate system, resamples to volume with 256x256x256 voxels (tri-linear by default, check https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all for more information).

2. Surface: Please use 'FreeSurfer' surfaces

3. Electrode registration and transforms This package provides two ways to map electrodes to standard space. For surface electrodes, if standard 141 brain is provided, then the first option is to snap electrodes to the nearest vertices in subject space. The key is the vertex number matches across different subjects, hence the location of corresponding vertices at template brain are the mapped electrode coordinates. If standard 141 brain is missing, or the electrode type is `stereo EEG`, then the second option is volume mapping. The idea is to map electrodes to `MNI305` brain. The details can be found at https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems. To perform volume mapping, we need `FreeSurfer` folder `mri/transforms`. Currently, only linear `Talairach` transform matrix is supported (located at `talairach.xfm`).

4. Coordinates The 3D viewer in this package uses the center of volume as the origin (0, 0, 0).

Author

Zhengjia Wang

Examples

if (FALSE) { # \dontrun{
# Please run `download_N27()` if `N27` is not at `default_template_directory()`

# Import from `FreeSurfer` subject folder
brain = threeBrain::freesurfer_brain(
  fs_subject_folder = file.path(default_template_directory(), 'N27'),
  subject_name = 'N27',
  additional_surfaces = c('white', 'smoothwm')
)

# Visualize. Alternatively, you can use brain$plot(...)
plot( brain )
} # }