Read and Write 'FreeSurfer' Neuroimaging File Formats

Documentation for package ‘freesurferformats’ version 1.1.0

Help Pages

-- A --

analyzeheader.for.data	Create ANALYZE 7.5 header suitable for given data.
analyzeheader.template	Create a template ANALYZE 7.5 header. You will have to adapt it for your use case.
annot.max.region.idx	Get max region index of an fs.annot instance.
as.fs.tracts	Convert a collection of tracts to an fs.tracts instance.
as.list.fs.tracts	Convert an fs.tracts instance to a plain list of tracts.
atlas.from.lut.and.csv	Construct a brain atlas from a colortable (LUT) file and a per-vertex label file.

-- B --

bvsmp

Create new bvsmp instance encoding morph data for Brainvoyager.

-- C --

cdata	Create CDATA element string from string.
cifti.axis.brain.models	Create a CIFTI-2 axis for brain models.
cifti.axis.from.template	Create a CIFTI-2 axis from a template file.
cifti.axis.labels	Create a CIFTI-2 axis for label maps.
cifti.axis.parcels	Create a CIFTI-2 axis for parcels.
cifti.axis.parcels.from.annot	Create a CIFTI-2 parcels axis from brain surface annotations.
cifti.axis.scalars	Create a CIFTI-2 axis for scalar or label maps.
cifti.axis.series	Create a CIFTI-2 axis for a series.
cifti.brain.model.surface	Create a CIFTI-2 brain model entry for a surface.
cifti.brain.model.volume	Create a CIFTI-2 brain model entry for volume voxels.
cifti.dim.labels	Get axis labels for a matrix dimension of a CIFTI-2 file.
cifti.file.type.for.axes	Get the standard CIFTI-2 file type for a set of axes.
cifti.grayordinates	Get the brainordinate table of a CIFTI-2 file.
cifti.header.from.axes	Create the CIFTI-2 XML metadata for a set of axes.
cifti.label.table	Get a label table from a CIFTI-2 label file.
cifti.parcel	Create a CIFTI-2 parcel.
cifti.parcels	Get the parcel table of a CIFTI-2 file.
cifti.series.info	Get the series information of a CIFTI-2 file.
cifti.structure.data	Extract the data of one brain structure from a CIFTI-2 file.
cifti.structures	Get the brain model table of a CIFTI-2 file.
cifti.volume	Create a CIFTI-2 axis for a volume.
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.
dti.track.bbox	Compute the bounding box of all tract coordinates in a file.
dti.track.count	Count the tracts in a DTI tract file.
dti.track.iterator	Create an iterator over the tracts of a DTI tract file.

-- 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.
fs.tracts	Create an fs.tracts instance from a compact tract representation.
fs.tracts.coords	Get the concatenated coordinates of fs.tracts instances.
fs.tracts.lengths	Get the number of points of each tract.

-- 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 --

invert.fs.transform	Invert a transformation.
is.analyze.file	Check whether a file is an ANALYZE 7.5 file.
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.tracts	Check whether an object is an fs.tracts instance.
is.fs.transform	Check whether an object is an fs.transform instance.
is.fs.volume	Check whether object is an fs.volume
is.mghheader	Check whether object is an mghheader

-- L --

length.fs.tracts	Number of tracts in an fs.tracts instance.
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.
nifti2.extension	Create a NIFTI v2 header extension.
nifti2.extension.text	Get the payload of a NIFTI v2 header extension as text.
nifti2.get.extension	Get a NIFTI v2 header extension by code.
nii1header.for.mgh	Create a NIFTI v1 header from the header information contained in an fs.volume instance.

-- P --

print.dti.track.iterator	Print a tract file iterator.
print.fs.annot	Print description of a brain atlas or annotation.
print.fs.cifti	Print an fs.cifti instance.
print.fs.cifti.data	Print an fs.cifti.data instance.
print.fs.connectome	Print an fs.connectome instance.
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.tracts	Print an fs.tracts instance.
print.fs.transform	Print an fs.transform instance.
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.analyze.data	Read ANALYZE 7.5 data from file.
read.analyze.header	Read ANALYZE 7.5 header from file.
read.cifti	Read a CIFTI-2 file.
read.cifti.header	Read CIFTI-2 header (XML metadata).
read.cifti.rows	Read selected matrix rows of a CIFTI-2 file without loading the whole matrix.
read.dti.bval	Read b-values from a FSL-style bvals file.
read.dti.bvec	Read b-vectors from a FSL-style bvecs file.
read.dti.grad	Read a gradient table in MRtrix3 format.
read.dti.gradients	Read and validate a diffusion MRI gradient table.
read.dti.tck	Read DTI tracking data from file in MRtrix 'TCK' format.
read.dti.tck.header	Read the header of a file in MRtrix 'TCK' or 'TSF' format.
read.dti.trk	Read fiber tracks from Diffusion Toolkit in trk format.
read.dti.trk.header	Read the header of a TrackVis TRK file.
read.dti.tsf	Read DTI tracking per-coord data from file in MRtrix 'TSF' format.
read.dti.tsf.header	Read the header of a 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.connectome.cifti	Read a CIFTI-2 connectome file.
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.parcellation.cifti	Read surface parcellation data from CIFTI dlabel files.
read.fs.patch	Read FreeSurfer binary or ASCII patch file.
read.fs.patch.asc	Read FreeSurfer ASCII format patch.
read.fs.series.cifti	Read surface time series data from CIFTI dtseries files.
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 legacy format mesh as surface.
read.fs.tracts.vtk	Read VTK legacy format streamlines as tracts.
read.fs.transform	Load transformation matrix from a file.
read.fs.transform.dat	Load transformation matrix from a tkregister dat file.
read.fs.transform.fslmat	Read a transformation matrix from an FSL matrix file.
read.fs.transform.itk	Read a transformation matrix from an ITK text transform 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.analyze	Read an ANALYZE 7.5 or NIFTI v1 pair file as an fs.volume.
read.fs.volume.nii	Read a 3D or 4D NIFTI file into an 'fs.volume' instance with complete header.
read.fs.volume.nrrd	Read volume data from a file in NRRD format.
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.nrrd.header	Read the header of a file in NRRD format.
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.
summary.fs.transform	Summarize an fs.transform instance.
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.
transform2lps	Convert a transformation to LPS world coordinates.
transform2ras	Convert a transformation to RAS world coordinates.
transform2voxel	Convert a transformation to voxel coordinates.
transform2world	Convert a transformation to the world (RAS) coordinate space.

-- 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.analyze	Write data to a file in ANALYZE 7.5 format.
write.atlas.to.lut.and.csv	Write a brain atlas to a colortable (LUT) file and a per-vertex label file.
write.cifti	Write a CIFTI-2 file.
write.dti.bval	Write b-values to a FSL-style bvals file.
write.dti.bvec	Write b-vectors to a FSL-style bvecs file.
write.dti.grad	Write a gradient table in MRtrix3 format.
write.dti.tck	Write tracks to a file in MRtrix TCK format.
write.dti.trk	Write tracks to a file in TrackVis TRK format.
write.dti.tsf	Write per-point track values to a file in MRtrix TSF format.
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.connectome.cifti	Write a CIFTI-2 connectome file.
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.cifti	Write morphometry data to a CIFTI-2 '.dscalar' file.
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.parcellated.cifti	Write a CIFTI-2 parcellated map or series file.
write.fs.parcellation.cifti	Write a parcellation to a CIFTI-2 '.dlabel' file.
write.fs.patch	Write a surface patch
write.fs.series.cifti	Write time series data to a CIFTI-2 '.dtseries' file.
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.stl	Write mesh to file in STL format (ASCII or binary).
write.fs.surface.vtk	Write mesh to file in VTK legacy format
write.fs.transform	Write a transformation matrix to a file.
write.fs.transform.dat	Write a tkregister dat file.
write.fs.transform.fslmat	Write a transformation matrix in FSL format.
write.fs.transform.itk	Write an ITK text transform file.
write.fs.transform.lta	Write a FreeSurfer linear transform array (LTA) file.
write.fs.transform.xfm	Write an MNI transform (xfm) file.
write.fs.volume	Write an fs.volume instance to a file in MGH, MGZ or NIFTI v1 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.

-- misc --

[.fs.tracts	Subset an fs.tracts instance.
[[.fs.tracts	Access a single tract of an fs.tracts instance.