Package index • freesurferformats

All functions

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.
bvsmp(): Create new bvsmp instance encoding morph data for Brainvoyager.
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.
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.
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.
get_opt_data_filepath(): Access a single file from the package cache by its file name.
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.
giftixml_add_labeltable_from_annot(): Add a label tabel from an annotation to a GIFTI XML tree.
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
length(<fs.tracts>): Number of tracts in an fs.tracts instance.
list_opt_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.
mni152reg(): Get fsaverage (MNI305) to MNI152 transformation matrix.
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.
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.
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.
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.
readable.files(): Find files with the given base name and extensions that exist.
rotate2D(): Rotate a 2D matrix in 90 degree steps.
rotate3D(): Rotate a 3D array in 90 degree steps.
sm0to1(): Adapt spatial transformation matrix for 1-based indices.
sm1to0(): Adapt spatial transformation matrix for 0-based indices.
`[`(<fs.tracts>): Subset an fs.tracts instance.
`[[`(<fs.tracts>): Access a single tract of an fs.tracts instance.
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).
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.
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.
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.
xml_node_gifti_coordtransform(): Create XML GIFTI CoordinateSystemTransformMatrix node.