read.fs.volume.nii: Turn a 3D or 4D `oro.nifti` instance into an `fs.volume` instance with complete header.

Description

This is work in progress. This function takes an oro.nifti instance and computes the MGH header fields from the NIFTI header data, allowing for proper orientation of the contained image data (see mghheader.vox2ras and related functions). Currently only few datatypes are supported, and the sform header field needs to be present in the NIFTI instance.

Usage

read.fs.volume.nii(
  filepath,
  flatten = FALSE,
  with_header = FALSE,
  drop_empty_dims = FALSE,
  do_rotate = FALSE,
  ...
)

Value

an fs.volume instance. The header fields are computed from the NIFTI header. The data array is rotated into FreeSurfer storage order, but otherwise returned as present in the input NIFTI instance, i.e., no values are changed in any way.

Arguments

filepath: instance of class nifti from the oro.nifti package, or a path to a NIFTI file as a character string.
flatten: logical. Whether to flatten the return volume to a 1D vector. Useful if you know that this file contains 1D morphometry data.
with_header: logical. Whether to return the header as well. If TRUE, return an instance of class fs.volume for data with at least 3 dimensions, a named list with entries "data" and "header". The latter is another named list which contains the header data. These header entries exist: "dtype": int, one of: 0=MRI_UCHAR; 1=MRI_INT; 3=MRI_FLOAT; 4=MRI_SHORT. "voldim": integer vector. The volume (=data) dimensions. E.g., c(256, 256, 256, 1). These header entries may exist: "vox2ras_matrix" (exists if "ras_good_flag" is 1), "mr_params" (exists if "has_mr_params" is 1). See the mghheader.* functions, like mghheader.vox2ras.tkreg, to compute more information from the header fields.
drop_empty_dims: logical, whether to drop empty dimensions of the returned data
do_rotate: logical, whether to rotate 3D volumes to compensate for storage order. WIP.
...: extra parameters passed to oro.nifti::readNIfTI. Leave this alone unless you know what you are doing.

References

See https://nifti.nimh.nih.gov/nifti-1/ for the NIfTI-1 data format spec.

Examples

Run this code

if (FALSE) {
base_file <- "~/data/subject1_only/subject1/mri/brain"
# missing file ext.
mgh_file <- paste(base_file, ".mgz", sep = "")
# the standard MGH/MGZ file
nii_file <- paste(base_file, ".nii", sep = "")
# NIFTI file generated with mri_convert
brain_mgh <- read.fs.mgh(mgh_file, with_header = TRUE)
brain_nii <- read.fs.volume.nii(nii_file, with_header = TRUE)
all(brain_nii$data == brain_mgh$data)
# output: TRUE
all(mghheader.vox2ras(brain_nii) == mghheader.vox2ras(brain_mgh)) # output: TRUE
}