read.fs.morph: Read morphometry data file in any FreeSurfer format.

In freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats

Read morphometry data file in any FreeSurfer format.

Description

Read vertex-wise brain surface data from a file. The file can be in any of the supported formats, and the format will be determined from the file extension.

Usage

read.fs.morph(filepath, format = "auto")

Arguments

filepath	string. Full path to the input file. The suffix determines the expected format as follows: ".mgz" and ".mgh" will be read with the read.fs.mgh function, all other file extensions will be read with the read.fs.curv function.
format	character string, the format to use. One of c("auto", "mgh", "mgz", "curv", "gii"). The default setting "auto" will determine the format from the file extension.

Value

data, vector of floats. The brain morphometry data, one value per vertex.

Note

CIFTI-2 files (which are NIFTI-2 files, see read.cifti) are refused with an error instead of being read as NIFTI morphometry data: their payload is a matrix whose dimensions the CIFTI XML metadata describes, so the values would come back in an order that means nothing. Use read.fs.morph.cifti to read the morphometry data of one brain structure, or read.cifti for the matrix itself.

See Also

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

Examples

curvfile <- system.file("extdata", "lh.thickness",
  package = "freesurferformats", mustWork = TRUE
)
ct <- read.fs.morph(curvfile)
cat(sprintf(
  "Read data for %d vertices. Values: min=%f, mean=%f, max=%f.\n",
  length(ct), min(ct), mean(ct), max(ct)
))
mghfile <- system.file("extdata", "lh.curv.fwhm10.fsaverage.mgz",
  package = "freesurferformats", mustWork = TRUE
)
curv <- read.fs.morph(mghfile)
cat(sprintf(
  "Read data for %d vertices. Values: min=%f, mean=%f, max=%f.\n",
  length(ct), min(ct), mean(ct), max(ct)
))

freesurferformats documentation built on Sept. 25, 2026, 1:07 a.m.