# Read and Write 'FreeSurfer' Neuroimaging File Formats

## Documentation for package ‘freesurferformats’ version 0.1.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

colortable.from.annot | Extract color lookup table (LUT) from annotation.
delete_all_optional_data | Delete all data in the package cache.
download_optional_data | Download optional data for the freesurferformats package.
fs.get.morph.file.ext.for.format | Determine morphometry file extension from format
fs.get.morph.file.format.from.filename | Determine morphometry file format from filename
fs.patch | Constructor for fs.patch
get_optional_data_filepath | Access a single file from the package cache by its file name.
is.fs.annot | Check whether object is an fs.annot
is.fs.label | Check whether object is an fs.label
is.fs.surface | Check whether object is an fs.surface
is.fs.volume | Check whether object is an fs.volume
list_optional_data | Get file names available in package cache.
mghheader.centervoxelRAS.from.firstvoxelRAS | Compute RAS coords of center voxel.
mghheader.crs.orientation | Compute MGH volume orientation string.
mghheader.is.conformed | Determine whether an MGH volume is conformed.
mghheader.is.ras.valid | Check whether header contains valid ras information
mghheader.primary.slice.direction | Compute MGH primary slice direction
mghheader.ras2vox | Compute ras2vox matrix from basic MGH header fields.
mghheader.ras2vox.tkreg | Compute ras2vox-tkreg matrix from basic MGH header fields.
mghheader.scanner2tkreg | Compute scanner-RAS 2 tkreg-RAS matrix from basic MGH header fields.
mghheader.tkreg2scanner | Compute tkreg-RAS to scanner-RAS matrix from basic MGH header fields.
mghheader.update.from.vox2ras | Update mghheader fields from vox2ras matrix.
mghheader.vox2ras | Compute vox2ras matrix from basic MGH header fields.
mghheader.vox2ras.tkreg | Compute vox2ras-tkreg matrix from basic MGH header fields.
mghheader.vox2vox | Compute vox2vox matrix between two volumes.
print.fs.annot | Print description of a brain atlas or annotation.
print.fs.label | Print description of a brain surface label.
print.fs.patch | Print description of a brain surface patch.
print.fs.surface | Print description of a brain surface.
print.fs.volume | Print description of a brain volume.
read.fs.annot | Read file in FreeSurfer annotation format
read.fs.colortable | Read colortable file in FreeSurfer ASCII LUT format.
read.fs.curv | Read file in FreeSurfer curv format
read.fs.label | Read file in FreeSurfer label format
read.fs.mgh | Read file in FreeSurfer MGH or MGZ format
read.fs.morph | Read morphometry data file in any FreeSurfer format.
read.fs.patch | Read FreeSurfer binary or ASCII patch file.
read.fs.patch.asc | Read FreeSurfer ASCII format patch.
read.fs.surface | Read file in FreeSurfer surface format
read.fs.surface.asc | Read FreeSurfer ASCII format surface.
read.fs.surface.vtk | Read VTK ASCII format mesh as surface.
read.fs.weight | Read file in FreeSurfer weight or w format
read_nisurface | Read a surface, based on the file path without extension.
read_nisurfacefile | S3 method to read a neuroimaging surface file.
read_nisurfacefile.fsascii | Read a FreeSurfer ASCII surface file.
read_nisurfacefile.fsnative | Read a FreeSurfer ASCII surface file.
read_nisurfacefile.gifti | Read a gifti file as a surface.
write.fs.annot | Write annotation to binary file.
write.fs.colortable | Write colortable file in FreeSurfer ASCII LUT format.
write.fs.curv | Write file in FreeSurfer curv format
write.fs.label | Write vertex indices to file in FreeSurfer label format
write.fs.mgh | Write file in FreeSurfer MGH or MGZ format
write.fs.morph | Write morphometry data in a format derived from the given file name (the file extension).
write.fs.patch | Write a surface patch
write.fs.surface | Write mesh to file in FreeSurfer binary surface format
write.fs.surface.asc | Write mesh to file in FreeSurfer ASCII surface format
write.fs.surface.vtk | Write mesh to file in VTK ASCII format
write.fs.weight | Write file in FreeSurfer weight format