read.fs.volume.nii | R Documentation |
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.
read.fs.volume.nii(
filepath,
flatten = FALSE,
with_header = FALSE,
drop_empty_dims = FALSE,
do_rotate = FALSE,
...
)
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 |
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 |
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.
This is not supposed to be used to read 1D morphometry data from NIFTI files generated by FreeSurfer (e.g., by converting 'lh.thickness' to NIFTI using 'mri_convert'): the FreeSurfer NIFTI hack is not supported by oro.nifti.
See https://nifti.nimh.nih.gov/nifti-1/ for the NIfTI-1 data format spec.
oro.nifti::readNIfTI
, read.fs.mgh
## Not run:
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
## End(Not run)
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