freesurferformats (version 0.1.18)

read.fs.mgh: Read file in FreeSurfer MGH or MGZ format

Description

Read multi-dimensional brain imaging data from a file in FreeSurfer binary MGH or MGZ format. The MGZ format is just a gzipped version of the MGH format. For a subject (MRI image pre-processed with FreeSurfer) named 'bert', an example file would be 'bert/mri/T1.mgz', which contains a 3D brain scan of bert.

Usage

read.fs.mgh(
  filepath,
  is_gzipped = "AUTO",
  flatten = FALSE,
  with_header = FALSE,
  drop_empty_dims = FALSE
)

Value

data, multi-dimensional array. The brain imaging data, one value per voxel. The data type and the dimensions depend on the data in the file, they are read from the header. If the parameter flatten is `TRUE`, a numeric vector is returned instead. Note: The return value changes if the parameter with_header is `TRUE`, see parameter description.

Arguments

filepath

string. Full path to the input MGZ or MGH file.

is_gzipped

a logical value or the string 'AUTO'. Whether to treat the input file as gzipped, i.e., MGZ instead of MGH format. Defaults to 'AUTO', which tries to determine this from the last three characters of the 'filepath' parameter. Files with extensions 'mgz' and '.gz' (in arbitrary case) are treated as MGZ format, all other files are treated as MGH. In the special case that 'filepath' has less than three characters, MGH is assumed.

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

See Also

To derive more information from the header, see the `mghheader.*` functions, like mghheader.vox2ras.tkreg.

Other morphometry functions: fs.get.morph.file.ext.for.format(), fs.get.morph.file.format.from.filename(), read.fs.curv(), read.fs.morph.gii(), read.fs.morph(), read.fs.volume(), read.fs.weight(), write.fs.curv(), write.fs.label.gii(), write.fs.mgh(), write.fs.morph.asc(), write.fs.morph.gii(), write.fs.morph.ni1(), write.fs.morph.ni2(), write.fs.morph.smp(), write.fs.morph.txt(), write.fs.morph(), write.fs.weight.asc(), write.fs.weight()

Examples

    brain_image = system.file("extdata", "brain.mgz",
                               package = "freesurferformats",
                               mustWork = TRUE);
    vd = read.fs.mgh(brain_image);
    cat(sprintf("Read voxel data with dimensions %s. Values: min=%d, mean=%f, max=%d.\n",
                 paste(dim(vd), collapse = ' '), min(vd), mean(vd), max(vd)));
    # Read it again with full header data:
    vdh = read.fs.mgh(brain_image, with_header = TRUE);
    # Use the vox2ras matrix from the header to compute RAS coordinates at CRS voxel (0, 0, 0):
    vdh$header$vox2ras_matrix %*% c(0,0,0,1);