| Subset an fs.tracts instance. | [.fs.tracts |
| Access a single tract of an fs.tracts instance. | [[.fs.tracts |
| Create ANALYZE 7.5 header suitable for given data. | analyzeheader.for.data |
| Create a template ANALYZE 7.5 header. You will have to adapt it for your use case. | analyzeheader.template |
| Get max region index of an fs.annot instance. | annot.max.region.idx |
| Convert a collection of tracts to an fs.tracts instance. | as.fs.tracts |
| Convert an fs.tracts instance to a plain list of tracts. | as.list.fs.tracts |
| Construct a brain atlas from a colortable (LUT) file and a per-vertex label file. | atlas.from.lut.and.csv |
| Create new bvsmp instance encoding morph data for Brainvoyager. | bvsmp |
| Create CDATA element string from string. | cdata |
| Create a CIFTI-2 axis for brain models. | cifti.axis.brain.models |
| Create a CIFTI-2 axis from a template file. | cifti.axis.from.template |
| Create a CIFTI-2 axis for label maps. | cifti.axis.labels |
| Create a CIFTI-2 axis for parcels. | cifti.axis.parcels |
| Create a CIFTI-2 parcels axis from brain surface annotations. | cifti.axis.parcels.from.annot |
| Create a CIFTI-2 axis for scalar or label maps. | cifti.axis.scalars |
| Create a CIFTI-2 axis for a series. | cifti.axis.series |
| Create a CIFTI-2 brain model entry for a surface. | cifti.brain.model.surface |
| Create a CIFTI-2 brain model entry for volume voxels. | cifti.brain.model.volume |
| Get axis labels for a matrix dimension of a CIFTI-2 file. | cifti.dim.labels |
| Get the standard CIFTI-2 file type for a set of axes. | cifti.file.type.for.axes |
| Get the brainordinate table of a CIFTI-2 file. | cifti.grayordinates |
| Create the CIFTI-2 XML metadata for a set of axes. | cifti.header.from.axes |
| Get a label table from a CIFTI-2 label file. | cifti.label.table |
| Create a CIFTI-2 parcel. | cifti.parcel |
| Get the parcel table of a CIFTI-2 file. | cifti.parcels |
| Get the series information of a CIFTI-2 file. | cifti.series.info |
| Extract the data of one brain structure from a CIFTI-2 file. | cifti.structure.data |
| Get the brain model table of a CIFTI-2 file. | cifti.structures |
| Create a CIFTI-2 axis for a volume. | cifti.volume |
| Find vertex index closest to given query coordinate using Euclidean distance. | closest.vert.to.point |
| Extract color lookup table (LUT) from annotation. | colortable.from.annot |
| Delete all data in the package cache. | delete_all_opt_data |
| Apply a spatial transformation matrix to the given coordinates. | doapply.transform.mtx |
| Download optional data for the freesurferformats package. | download_opt_data |
| Compute the bounding box of all tract coordinates in a file. | dti.track.bbox |
| Count the tracts in a DTI tract file. | dti.track.count |
| Create an iterator over the tracts of a DTI tract file. | dti.track.iterator |
| Convert quadrangular faces or polygons to triangular ones. | faces.quad.to.tris |
| Convert tris faces to quad faces by simple merging. | faces.tris.to.quad |
| Flip a 2D matrix. | flip2D |
| Flip a 3D array along an axis. | flip3D |
| Determine morphometry file extension from format | fs.get.morph.file.ext.for.format |
| Determine morphometry file format from filename | fs.get.morph.file.format.from.filename |
| Constructor for fs.patch | fs.patch |
| Get an rgl tmesh3d instance from a brain surface mesh. | fs.surface.to.tmesh3d |
| Create an fs.tracts instance from a compact tract representation. | fs.tracts |
| Get the concatenated coordinates of fs.tracts instances. | fs.tracts.coords |
| Get the number of points of each tract. | fs.tracts.lengths |
| Access a single file from the package cache by its file name. | get_opt_data_filepath |
| Write data to a gifti file. | gifti_writer |
| Get GIFTI XML representation of data. | gifti_xml |
| Add metadata to GIFTI XML tree. | gifti_xml_add_global_metadata |
| Write XML tree to a gifti file. | gifti_xml_write |
| Add a label tabel from an annotation to a GIFTI XML tree. | giftixml_add_labeltable_from_annot |
| Invert a transformation. | invert.fs.transform |
| Check whether a file is an ANALYZE 7.5 file. | is.analyze.file |
| Check whether object is a bvsmp instance. | is.bvsmp |
| Check whether object is an fs.annot | is.fs.annot |
| Check whether object is an fs.label | is.fs.label |
| Check whether object is an fs.surface | is.fs.surface |
| Check whether an object is an fs.tracts instance. | is.fs.tracts |
| Check whether an object is an fs.transform instance. | is.fs.transform |
| Check whether object is an fs.volume | is.fs.volume |
| Check whether object is an mghheader | is.mghheader |
| Number of tracts in an fs.tracts instance. | length.fs.tracts |
| Get file names available in package cache. | list_opt_data |
| Compute RAS coords of center voxel. | mghheader.centervoxelRAS.from.firstvoxelRAS |
| Compute MGH volume orientation string. | mghheader.crs.orientation |
| Determine whether an MGH volume is conformed. | mghheader.is.conformed |
| Check whether header contains valid ras information | mghheader.is.ras.valid |
| Compute MGH primary slice direction | mghheader.primary.slice.direction |
| Compute ras2vox matrix from basic MGH header fields. | mghheader.ras2vox |
| Compute ras2vox-tkreg matrix from basic MGH header fields. | mghheader.ras2vox.tkreg |
| Compute scanner-RAS 2 tkreg-RAS matrix from basic MGH header fields. | mghheader.scanner2tkreg |
| Compute tkreg-RAS to scanner-RAS matrix from basic MGH header fields. | mghheader.tkreg2scanner |
| Update mghheader fields from vox2ras matrix. | mghheader.update.from.vox2ras |
| Compute vox2ras matrix from basic MGH header fields. | mghheader.vox2ras |
| Compute vox2ras-tkreg matrix from basic MGH header fields. | mghheader.vox2ras.tkreg |
| Compute vox2vox matrix between two volumes. | mghheader.vox2vox |
| Get fsaverage (MNI305) to MNI152 transformation matrix. | mni152reg |
| Create NIFTI v1 header suitable for given data. | ni1header.for.data |
| Create a template NIFTI v1 header. You will have to adapt it for your use case. | ni1header.template |
| Create NIFTI v2 header suitable for given data. | ni2header.for.data |
| Create a template NIFTI v2 header. You will have to adapt it for your use case. | ni2header.template |
| Compute data dimensions from the 'dim' field of the NIFTI (v1 or v2) header. | nifti.datadim.from.dimfield |
| Compute NIFTI dim field for data dimension. | nifti.datadim.to.dimfield |
| Determine whether a NIFTI file uses the FreeSurfer hack. | nifti.file.uses.fshack |
| Determine NIFTI file version information and whether file is a NIFTI file. | nifti.file.version |
| Perform basic sanity checks on NIFTI header data. These are in no way meant to be exhaustive. | nifti.header.check |
| Create a NIFTI v2 header extension. | nifti2.extension |
| Get the payload of a NIFTI v2 header extension as text. | nifti2.extension.text |
| Get a NIFTI v2 header extension by code. | nifti2.get.extension |
| Create a NIFTI v1 header from the header information contained in an fs.volume instance. | nii1header.for.mgh |
| Print a tract file iterator. | print.dti.track.iterator |
| Print description of a brain atlas or annotation. | print.fs.annot |
| Print an fs.cifti instance. | print.fs.cifti |
| Print an fs.cifti.data instance. | print.fs.cifti.data |
| Print an fs.connectome instance. | print.fs.connectome |
| Print description of a brain surface label. | print.fs.label |
| Print description of a brain surface patch. | print.fs.patch |
| Print description of a brain surface. | print.fs.surface |
| Print an fs.tracts instance. | print.fs.tracts |
| Print an fs.transform instance. | print.fs.transform |
| Print description of a brain volume. | print.fs.volume |
| Translate RAS coordinates, as used in volumes by applying vox2ras, to surface RAS. | ras.to.surfaceras |
| Compute MNI talairach coordinates from RAS coords. | ras.to.talairachras |
| Read a surface, based on the file path without extension. | read_nisurface |
| S3 method to read a neuroimaging surface file. | read_nisurfacefile |
| Read a FreeSurfer ASCII surface file. | read_nisurfacefile.fsascii |
| Read a FreeSurfer ASCII surface file. | read_nisurfacefile.fsnative |
| Read a gifti file as a surface. | read_nisurfacefile.gifti |
| Read ANALYZE 7.5 data from file. | read.analyze.data |
| Read ANALYZE 7.5 header from file. | read.analyze.header |
| Read a CIFTI-2 file. | read.cifti |
| Read CIFTI-2 header (XML metadata). | read.cifti.header |
| Read selected matrix rows of a CIFTI-2 file without loading the whole matrix. | read.cifti.rows |
| Read b-values from a FSL-style bvals file. | read.dti.bval |
| Read b-vectors from a FSL-style bvecs file. | read.dti.bvec |
| Read a gradient table in MRtrix3 format. | read.dti.grad |
| Read and validate a diffusion MRI gradient table. | read.dti.gradients |
| Read DTI tracking data from file in MRtrix 'TCK' format. | read.dti.tck |
| Read the header of a file in MRtrix 'TCK' or 'TSF' format. | read.dti.tck.header |
| Read fiber tracks from Diffusion Toolkit in trk format. | read.dti.trk |
| Read the header of a TrackVis TRK file. | read.dti.trk.header |
| Read DTI tracking per-coord data from file in MRtrix 'TSF' format. | read.dti.tsf |
| Read the header of a file in MRtrix 'TSF' format. | read.dti.tsf.header |
| Read file in FreeSurfer annotation format | read.fs.annot |
| Read an annotation or label in GIFTI format. | read.fs.annot.gii |
| Read colortable file in FreeSurfer ASCII LUT format. | read.fs.colortable |
| Read a CIFTI-2 connectome file. | read.fs.connectome.cifti |
| Read file in FreeSurfer curv format | read.fs.curv |
| Read FreeSurfer GCA file. | read.fs.gca |
| Read a label file. | read.fs.label |
| Read a label from a GIFTI label/annotation file. | read.fs.label.gii |
| Read file in FreeSurfer label format | read.fs.label.native |
| Read file in FreeSurfer MGH or MGZ format | read.fs.mgh |
| Read morphometry data file in any FreeSurfer format. | read.fs.morph |
| Read morphometry data from ASCII curv format file | read.fs.morph.asc |
| Read Brainvoyager vertex-wise statistical surface data from SMP file. | read.fs.morph.bvsmp |
| Read surface morphometry data from CIFTI dscalar files. | read.fs.morph.cifti |
| Read morphometry data file in GIFTI format. | read.fs.morph.gii |
| Read morphometry data from FreeSurfer NIFTI v1 format files. | read.fs.morph.ni1 |
| Read morphometry data from FreeSurfer NIFTI v2 format files. | read.fs.morph.ni2 |
| Read morphometry data from FreeSurfer NIFTI format files, determine NIFTI version automatically. | read.fs.morph.nii |
| Read morphometry data from plain text file | read.fs.morph.txt |
| Read surface parcellation data from CIFTI dlabel files. | read.fs.parcellation.cifti |
| Read FreeSurfer binary or ASCII patch file. | read.fs.patch |
| Read FreeSurfer ASCII format patch. | read.fs.patch.asc |
| Read surface time series data from CIFTI dtseries files. | read.fs.series.cifti |
| Read file in FreeSurfer surface format or various mesh formats. | read.fs.surface |
| Read FreeSurfer ASCII format surface. | read.fs.surface.asc |
| Read Brainvoyager srf format (.srf) mesh as surface. | read.fs.surface.bvsrf |
| Read mesh in BYU format. | read.fs.surface.byu |
| Read GEO format mesh as surface. | read.fs.surface.geo |
| Read GIFTI format mesh as surface. | read.fs.surface.gii |
| Read ICO format mesh as surface. | read.fs.surface.ico |
| Read surface mesh in mz3 format, used by Surf-Ice. | read.fs.surface.mz3 |
| Read OBJ format mesh as surface. | read.fs.surface.obj |
| Read Object File Format (OFF) mesh as surface. | read.fs.surface.off |
| Read Stanford PLY format mesh as surface. | read.fs.surface.ply |
| Read mesh in STL format, auto-detecting ASCII versus binary format version. | read.fs.surface.stl |
| Read surface mesh in STL binary format. | read.fs.surface.stl.bin |
| Read VTK legacy format mesh as surface. | read.fs.surface.vtk |
| Read VTK legacy format streamlines as tracts. | read.fs.tracts.vtk |
| Load transformation matrix from a file. | read.fs.transform |
| Load transformation matrix from a tkregister dat file. | read.fs.transform.dat |
| Read a transformation matrix from an FSL matrix file. | read.fs.transform.fslmat |
| Read a transformation matrix from an ITK text transform file. | read.fs.transform.itk |
| Load transformation matrix from a FreeSurfer linear transform array (LTA) file. | read.fs.transform.lta |
| Load transformation matrix from an XFM file. | read.fs.transform.xfm |
| Read volume file in MGH, MGZ or NIFTI format | read.fs.volume |
| Read an ANALYZE 7.5 or NIFTI v1 pair file as an fs.volume. | read.fs.volume.analyze |
| Read a 3D or 4D NIFTI file into an 'fs.volume' instance with complete header. | read.fs.volume.nii |
| Read volume data from a file in NRRD format. | read.fs.volume.nrrd |
| Read file in FreeSurfer weight or w format | read.fs.weight |
| Read Brainvoyager srf format (.srf) mesh. | read.mesh.brainvoyager |
| Read raw NIFTI v1 data from file (which may contain the FreeSurfer hack). | read.nifti1.data |
| Read NIFTI v1 header from file (which may contain the FreeSurfer hack). | read.nifti1.header |
| Read raw data from NIFTI v2 file. | read.nifti2.data |
| Read NIFTI v2 header from file. | read.nifti2.header |
| Read the header of a file in NRRD format. | read.nrrd.header |
| Read Brainvoyager statistical surface results from SMP file. | read.smp.brainvoyager |
| Find files with the given base name and extensions that exist. | readable.files |
| Rotate a 2D matrix in 90 degree steps. | rotate2D |
| Rotate a 3D array in 90 degree steps. | rotate3D |
| Adapt spatial transformation matrix for 1-based indices. | sm0to1 |
| Adapt spatial transformation matrix for 0-based indices. | sm1to0 |
| Summarize an fs.transform instance. | summary.fs.transform |
| Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS. | surfaceras.to.ras |
| Compute Talairach RAS for surface RAS (e.g., vertex coordinates). | surfaceras.to.talairach |
| Compute MNI talairach coordinates from RAS coords. | talairachras.to.ras |
| Convert a transformation to LPS world coordinates. | transform2lps |
| Convert a transformation to RAS world coordinates. | transform2ras |
| Convert a transformation to voxel coordinates. | transform2voxel |
| Convert a transformation to the world (RAS) coordinate space. | transform2world |
| Compute Euclidean distance between two vertices v1 and v2. | vertex.euclid.dist |
| Compute Euclidean distance from all mesh vertices to given point. | vertexdists.to.point |
| Write data to a file in ANALYZE 7.5 format. | write.analyze |
| Write a brain atlas to a colortable (LUT) file and a per-vertex label file. | write.atlas.to.lut.and.csv |
| Write a CIFTI-2 file. | write.cifti |
| Write b-values to a FSL-style bvals file. | write.dti.bval |
| Write b-vectors to a FSL-style bvecs file. | write.dti.bvec |
| Write a gradient table in MRtrix3 format. | write.dti.grad |
| Write tracks to a file in MRtrix TCK format. | write.dti.tck |
| Write tracks to a file in TrackVis TRK format. | write.dti.trk |
| Write per-point track values to a file in MRtrix TSF format. | write.dti.tsf |
| Write annotation to binary file. | write.fs.annot |
| Write annotation to GIFTI file. | write.fs.annot.gii |
| Write colortable file in FreeSurfer ASCII LUT format. | write.fs.colortable |
| Write a CIFTI-2 connectome file. | write.fs.connectome.cifti |
| Write file in FreeSurfer curv format | write.fs.curv |
| Write vertex indices to file in FreeSurfer label format | write.fs.label |
| Write a binary surface label in GIFTI format. | write.fs.label.gii |
| Write file in FreeSurfer MGH or MGZ format | write.fs.mgh |
| Write morphometry data in a format derived from the given file name. | write.fs.morph |
| Write file in FreeSurfer ASCII curv format | write.fs.morph.asc |
| Write morphometry data to a CIFTI-2 '.dscalar' file. | write.fs.morph.cifti |
| Write morphometry data in GIFTI format. | write.fs.morph.gii |
| Write morphometry data in NIFTI v1 format. | write.fs.morph.ni1 |
| Write morphometry data in NIFTI v2 format. | write.fs.morph.ni2 |
| Write morphometry data in Brainvoyager SMP format. | write.fs.morph.smp |
| Write curv data to file in simple text format | write.fs.morph.txt |
| Write a CIFTI-2 parcellated map or series file. | write.fs.parcellated.cifti |
| Write a parcellation to a CIFTI-2 '.dlabel' file. | write.fs.parcellation.cifti |
| Write a surface patch | write.fs.patch |
| Write time series data to a CIFTI-2 '.dtseries' file. | write.fs.series.cifti |
| Write mesh to file in FreeSurfer binary surface format | write.fs.surface |
| Write mesh to file in FreeSurfer ASCII surface format | write.fs.surface.asc |
| Write surface to Brainvoyager SRF file. | write.fs.surface.bvsrf |
| Write mesh to file in BYU ASCII format. | write.fs.surface.byu |
| Write mesh to file in GIFTI surface format | write.fs.surface.gii |
| Write mesh to file in mz3 binary format. | write.fs.surface.mz3 |
| Write mesh to file in Wavefront object (.obj) format | write.fs.surface.obj |
| Write mesh to file in Object File Format (.off) | write.fs.surface.off |
| Write mesh to file in PLY format (.ply) | write.fs.surface.ply |
| Write mesh to file in PLY2 File Format (.ply2) | write.fs.surface.ply2 |
| Write mesh to file in STL format (ASCII or binary). | write.fs.surface.stl |
| Write mesh to file in VTK legacy format | write.fs.surface.vtk |
| Write a transformation matrix to a file. | write.fs.transform |
| Write a tkregister dat file. | write.fs.transform.dat |
| Write a transformation matrix in FSL format. | write.fs.transform.fslmat |
| Write an ITK text transform file. | write.fs.transform.itk |
| Write a FreeSurfer linear transform array (LTA) file. | write.fs.transform.lta |
| Write an MNI transform (xfm) file. | write.fs.transform.xfm |
| Write an fs.volume instance to a file in MGH, MGZ or NIFTI v1 format. | write.fs.volume |
| Write file in FreeSurfer weight format | write.fs.weight |
| Write file in FreeSurfer weight ASCII format | write.fs.weight.asc |
| Write header and data to a file in NIFTI v1 format. | write.nifti1 |
| Write header and data to a file in NIFTI v2 format. | write.nifti2 |
| Write a brainvoyager SMP file. | write.smp.brainvoyager |
| Create XML GIFTI CoordinateSystemTransformMatrix node. | xml_node_gifti_coordtransform |
