Read and Write 'FreeSurfer' Neuroimaging File Formats

Documentation for package ‘freesurferformats’ version 0.1.18

Help Pages

A B C D F G I L M N P R S T V W X

-- A --

annot.max.region.idx

Get max region index of an fs.annot instance.

-- B --

bvsmp

Create new bvsmp instance encoding morph data for Brainvoyager.

-- C --

cdata	Create CDATA element string from string.
closest.vert.to.point	Find vertex index closest to given query coordinate using Euclidean distance.
colortable.from.annot	Extract color lookup table (LUT) from annotation.

-- D --

delete_all_opt_data	Delete all data in the package cache.
doapply.transform.mtx	Apply a spatial transformation matrix to the given coordinates.
download_opt_data	Download optional data for the freesurferformats package.

-- F --

faces.quad.to.tris	Convert quadrangular faces or polygons to triangular ones.
faces.tris.to.quad	Convert tris faces to quad faces by simple merging.
flip2D	Flip a 2D matrix.
flip3D	Flip a 3D array along an axis.
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
fs.surface.to.tmesh3d	Get an rgl tmesh3d instance from a brain surface mesh.

-- G --

get_opt_data_filepath	Access a single file from the package cache by its file name.
giftixml_add_labeltable_from_annot	Add a label tabel from an annotation to a GIFTI XML tree.
gifti_writer	Write data to a gifti file.
gifti_xml	Get GIFTI XML representation of data.
gifti_xml_add_global_metadata	Add metadata to GIFTI XML tree.
gifti_xml_write	Write XML tree to a gifti file.

-- I --

is.bvsmp	Check whether object is a bvsmp instance.
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
is.mghheader	Check whether object is an mghheader

-- L --

list_opt_data

Get file names available in package cache.

-- M --

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.
mni152reg	Get fsaverage (MNI305) to MNI152 transformation matrix.

-- N --

ni1header.for.data	Create NIFTI v1 header suitable for given data.
ni1header.template	Create a template NIFTI v1 header. You will have to adapt it for your use case.
ni2header.for.data	Create NIFTI v2 header suitable for given data.
ni2header.template	Create a template NIFTI v2 header. You will have to adapt it for your use case.
nifti.datadim.from.dimfield	Compute data dimensions from the 'dim' field of the NIFTI (v1 or v2) header.
nifti.datadim.to.dimfield	Compute NIFTI dim field for data dimension.
nifti.file.uses.fshack	Determine whether a NIFTI file uses the FreeSurfer hack.
nifti.file.version	Determine NIFTI file version information and whether file is a NIFTI file.
nifti.header.check	Perform basic sanity checks on NIFTI header data. These are in no way meant to be exhaustive.

-- P --

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.

-- R --

ras.to.surfaceras	Translate RAS coordinates, as used in volumes by applying vox2ras, to surface RAS.
ras.to.talairachras	Compute MNI talairach coordinates from RAS coords.
read.dti.tck	Read DTI tracking data from file in MRtrix 'TCK' format.
read.dti.trk	Read fiber tracks from Diffusion Toolkit in trk format.
read.dti.tsf	Read DTI tracking per-coord data from file in MRtrix 'TSF' format.
read.fs.annot	Read file in FreeSurfer annotation format
read.fs.annot.gii	Read an annotation or label in GIFTI format.
read.fs.colortable	Read colortable file in FreeSurfer ASCII LUT format.
read.fs.curv	Read file in FreeSurfer curv format
read.fs.gca	Read FreeSurfer GCA file.
read.fs.label	Read a label file.
read.fs.label.gii	Read a label from a GIFTI label/annotation file.
read.fs.label.native	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.morph.asc	Read morphometry data from ASCII curv format file
read.fs.morph.bvsmp	Read Brainvoyager vertex-wise statistical surface data from SMP file.
read.fs.morph.cifti	Read surface morphometry data from CIFTI dscalar files.
read.fs.morph.gii	Read morphometry data file in GIFTI format.
read.fs.morph.ni1	Read morphometry data from FreeSurfer NIFTI v1 format files.
read.fs.morph.ni2	Read morphometry data from FreeSurfer NIFTI v2 format files.
read.fs.morph.nii	Read morphometry data from FreeSurfer NIFTI format files, determine NIFTI version automatically.
read.fs.morph.txt	Read morphometry data from plain text file
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 or various mesh formats.
read.fs.surface.asc	Read FreeSurfer ASCII format surface.
read.fs.surface.bvsrf	Read Brainvoyager srf format (.srf) mesh as surface.
read.fs.surface.byu	Read mesh in BYU format.
read.fs.surface.geo	Read GEO format mesh as surface.
read.fs.surface.gii	Read GIFTI format mesh as surface.
read.fs.surface.ico	Read ICO format mesh as surface.
read.fs.surface.mz3	Read surface mesh in mz3 format, used by Surf-Ice.
read.fs.surface.obj	Read OBJ format mesh as surface.
read.fs.surface.off	Read Object File Format (OFF) mesh as surface.
read.fs.surface.ply	Read Stanford PLY format mesh as surface.
read.fs.surface.stl	Read mesh in STL format, auto-detecting ASCII versus binary format version.
read.fs.surface.stl.bin	Read surface mesh in STL binary format.
read.fs.surface.vtk	Read VTK ASCII format mesh as surface.
read.fs.transform	Load transformation matrix from a file.
read.fs.transform.dat	Load transformation matrix from a tkregister dat file.
read.fs.transform.lta	Load transformation matrix from a FreeSurfer linear transform array (LTA) file.
read.fs.transform.xfm	Load transformation matrix from an XFM file.
read.fs.volume	Read volume file in MGH, MGZ or NIFTI format
read.fs.volume.nii	Turn a 3D or 4D 'oro.nifti' instance into an 'fs.volume' instance with complete header.
read.fs.weight	Read file in FreeSurfer weight or w format
read.mesh.brainvoyager	Read Brainvoyager srf format (.srf) mesh.
read.nifti1.data	Read raw NIFTI v1 data from file (which may contain the FreeSurfer hack).
read.nifti1.header	Read NIFTI v1 header from file (which may contain the FreeSurfer hack).
read.nifti2.data	Read raw data from NIFTI v2 file.
read.nifti2.header	Read NIFTI v2 header from file.
read.smp.brainvoyager	Read Brainvoyager statistical surface results from SMP file.
readable.files	Find files with the given base name and extensions that exist.
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.
rotate2D	Rotate a 2D matrix in 90 degree steps.
rotate3D	Rotate a 3D array in 90 degree steps.

-- S --

sm0to1	Adapt spatial transformation matrix for 1-based indices.
sm1to0	Adapt spatial transformation matrix for 0-based indices.
surfaceras.to.ras	Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS.
surfaceras.to.talairach	Compute Talairach RAS for surface RAS (e.g., vertex coordinates).

-- T --

talairachras.to.ras

Compute MNI talairach coordinates from RAS coords.

-- V --

vertex.euclid.dist	Compute Euclidean distance between two vertices v1 and v2.
vertexdists.to.point	Compute Euclidean distance from all mesh vertices to given point.

-- W --

write.fs.annot	Write annotation to binary file.
write.fs.annot.gii	Write annotation to GIFTI 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.label.gii	Write a binary surface label in GIFTI 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.
write.fs.morph.asc	Write file in FreeSurfer ASCII curv format
write.fs.morph.gii	Write morphometry data in GIFTI format.
write.fs.morph.ni1	Write morphometry data in NIFTI v1 format.
write.fs.morph.ni2	Write morphometry data in NIFTI v2 format.
write.fs.morph.smp	Write morphometry data in Brainvoyager SMP format.
write.fs.morph.txt	Write curv data to file in simple text format
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.bvsrf	Write surface to Brainvoyager SRF file.
write.fs.surface.byu	Write mesh to file in BYU ASCII format.
write.fs.surface.gii	Write mesh to file in GIFTI surface format
write.fs.surface.mz3	Write mesh to file in mz3 binary format.
write.fs.surface.obj	Write mesh to file in Wavefront object (.obj) format
write.fs.surface.off	Write mesh to file in Object File Format (.off)
write.fs.surface.ply	Write mesh to file in PLY format (.ply)
write.fs.surface.ply2	Write mesh to file in PLY2 File Format (.ply2)
write.fs.surface.vtk	Write mesh to file in VTK ASCII format
write.fs.weight	Write file in FreeSurfer weight format
write.fs.weight.asc	Write file in FreeSurfer weight ASCII format
write.nifti1	Write header and data to a file in NIFTI v1 format.
write.nifti2	Write header and data to a file in NIFTI v2 format.
write.smp.brainvoyager	Write a brainvoyager SMP file.

-- X --

xml_node_gifti_coordtransform

Create XML GIFTI CoordinateSystemTransformMatrix node.