| adjust.face.indices.to | Adjust integer matrix to target min value. |
| analyze.dtype.info | Compute the R data type and the number of bytes per value for... |
| analyze.header.check | Check whether an ANALYZE 7.5 header is suitable for writing. |
| 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... |
| analyze.header.to.vox2ras | Compute a transformation matrix from the fields of an ANALYZE... |
| analyze.mat.sidecar.to.vox2ras | Compute the voxel-to-RAS matrix from the MATLAB sidecar file... |
| analyze.pair.files | Determine the header and data file of an ANALYZE 7.5 or NIFTI... |
| analyze.read.char.field | Read a fixed length character field of an ANALYZE 7.5 header. |
| analyze.read.header.internal | Read ANALYZE 7.5 header from file. |
| analyze.read.magic | Read the 4 magic bytes of an ANALYZE 7.5 or NIFTI v1 header. |
| analyze.write.data.internal | Write the voxel data of an ANALYZE 7.5 image to a connection. |
| annot.max.region.idx | Get max region index of an fs.annot instance. |
| annot.unique | Make the region names and indices unique across hemispheres... |
| apply.affine.to.coords | Apply an affine to a set of coordinates. |
| 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. |
| assert.surface | Stop unless surf is an fs.surface |
| as.tsf.scalars | Convert scalar values for streamlines to a list of vectors. |
| atlas.from.lut.and.csv | Construct a brain atlas from a colortable (LUT) file and a... |
| axcodes2ornt | Convert axis codes to an orientation array. |
| build.mrtrix.header | Build the text header of an MRtrix streamlines file. |
| build.mrtrix.header.stable | Determine the length of an MRtrix streamlines header. |
| bvsmp | Create new bvsmp instance encoding morph data for... |
| cdata | Create CDATA element string from string. |
| check_all_finite | Check that a numeric vector or matrix contains only finite... |
| check_data_and_settings_consistency | Warn about common errors in combining data and datatype. |
| check.dtype.for.data | Check whether the dtype is suitable for the data. |
| check_file_size | Check that a file is large enough to contain the expected... |
| cifti.annot.list | Accept the input forms of a set of annotations. |
| cifti.annot.parcels | Collect the vertices of each region of an annotation. |
| cifti.array.with.new.first.dim | Create an array like the input, with a different first... |
| cifti.assign.rows | Assign rows of an array, reordered or repeated. |
| cifti.axes.to.maps | Group axes into MatrixIndicesMap elements. |
| cifti.axis.brain.models | Create a CIFTI-2 axis for brain models. |
| cifti.axis.for.maps | Build the axis for a set of maps. |
| 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.named.maps | Create a CIFTI-2 axis for named maps (internal helper). |
| 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.axis.size | The number of matrix entries an axis covers. |
| cifti.axis.surfaces | Create the Surface elements of an axis. |
| cifti.axis.surface.sizes | Get the surface sizes of an axis as a named vector. |
| 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.brainordinate.dim | Get the brainordinate dimension of a CIFTI-2 file. |
| cifti.brainordinate.dims | Get all matrix dimensions of a CIFTI-2 file that hold brain... |
| cifti.check.axes | Check a list of axes and name the dimensions. |
| cifti.check.data.for.axes | Check and prepare the data for a set of axes. |
| cifti.check.index.list | Check a vector of 0-based indices. |
| cifti.check.index.selection | Check a matrix index selection. |
| cifti.check.label.table | Check a label table for writing. |
| cifti.check.object | Check that an object is an fs.cifti instance. |
| cifti.compute.index.ranges | Compute the index ranges of brain model entries. |
| cifti.connectome.axes | Determine the two axes of a connectome file. |
| cifti.data.for.all.vertices | Assemble the data values of all vertices for a file without a... |
| cifti.data.for.connectome | Accept the input forms of a CIFTI-2 connectome. |
| cifti.data.for.grayordinates | Select the data values of the grayordinates of a file. |
| cifti.data.object | Accept the input forms of a CIFTI-2 data object. |
| cifti.data.per.structure | Get the per-structure data of one structure. |
| cifti.data.structures | Determine the structures of per-vertex data. |
| cifti.data.surface.size | The number of vertices of the surface of one structure. |
| cifti.dense.structure.matrix | Get the dense data matrix of one structure for the... |
| cifti.dim.labels | Get axis labels for a matrix dimension of a CIFTI-2 file. |
| cifti.dim.to.front | Move one dimension of an array to the front. |
| CIFTI_EXTENSION_CODE | The NIFTI v2 extension code that holds the CIFTI-2 XML... |
| cifti.file.looks.like.cifti1 | Check whether a file looks like a CIFTI-1 file. |
| cifti.file.looks.like.cifti2 | Check whether a file is a CIFTI-2 file (internal helper). |
| cifti.file.type.for.axes | Get the standard CIFTI-2 file type for a set of axes. |
| cifti.file.type.for.extension | The CIFTI-2 file type a file name names. |
| cifti.file.types | The standard CIFTI-2 file types. |
| cifti.grayordinates | Get the brainordinate table of a CIFTI-2 file. |
| cifti.grayordinates.for.axes | Build the brainordinate table of an axis. |
| cifti.grayordinates.for.model | Expand one brain model entry into a brainordinate table. |
| cifti.header.from.axes | Create the CIFTI-2 XML metadata for a set of axes. |
| cifti.header.of | Accept the input forms of a CIFTI-2 header. |
| cifti.index.types | The CIFTI-2 index types (mapping types). |
| cifti.index.type.short | The short name of a CIFTI-2 matrix index type. |
| cifti.is.connectome.axis | Check whether an axis describes a connectome dimension. |
| cifti.label.table | Get a label table from a CIFTI-2 label file. |
| cifti.label.table.for.writing | Convert a label table to the format the writer expects. |
| cifti.map.for.dim | Get the CIFTI indices map for a matrix dimension. |
| cifti.map.name | Get the name of one named map of a CIFTI-2 file. |
| cifti.map.type.description | Describe a CIFTI-2 index type for humans. |
| cifti.matrix.dim.sizes | Determine the sizes of the CIFTI matrix dimensions. |
| cifti.merge.axes | Merge explicitly given axes with the axes of a template. |
| cifti.model.types | The CIFTI-2 brain model types. |
| cifti.nifti.header.for.axes | Build the NIFTI-2 header of a CIFTI-2 file. |
| cifti.other.dim | Get the other matrix dimension of a 2-dimensional CIFTI-2... |
| cifti.parcel | Create a CIFTI-2 parcel. |
| cifti.parcels | Get the parcel table of a CIFTI-2 file. |
| cifti.parcels.axis.of | Get the parcels axis of a template file. |
| cifti.parse.attr | Read and validate an attribute value of an XML node. |
| cifti.parse.brain.models | Parse the BrainModel elements of a MatrixIndicesMap element. |
| cifti.parse.child.int.vector | Parse a required or optional child element holding integer... |
| cifti.parse.child.voxel.indices | Parse the optionally present VoxelIndicesIJK child element as... |
| cifti.parse.indices.map | Parse one MatrixIndicesMap element. |
| cifti.parse.int.vector | Parse a whitespace-separated list of integers from XML text... |
| cifti.parse.label.table | Parse a CIFTI LabelTable element. |
| cifti.parse.metadata | Parse the MetaData element of a CIFTI XML node. |
| cifti.parse.named.maps | Parse the NamedMap elements of a MatrixIndicesMap element. |
| cifti.parse.numeric.vector | Parse a whitespace-separated list of numbers from XML text... |
| cifti.parse.parcels | Parse the Parcel elements of a MatrixIndicesMap element. |
| cifti.parse.series | Parse the series attributes of a MatrixIndicesMap element. |
| cifti.parse.surfaces | Parse the Surface elements of a MatrixIndicesMap element. |
| cifti.parse.volumes | Parse the Volume elements of a MatrixIndicesMap element. |
| cifti.parse.xml | Parse the CIFTI XML metadata. |
| cifti.prepare.surface.data | Prepare per-vertex data for writing to a CIFTI-2 file. |
| cifti.read.matrix | Read the data matrix of a CIFTI-2 file. |
| cifti.read.rows | Read the requested matrix rows of a CIFTI-2 file. |
| cifti.read.values | Read raw values from the data section of a CIFTI-2 file. |
| cifti.region.name.without.hemisphere | Remove hemisphere markers from region names of a... |
| cifti.series.info | Get the series information of a CIFTI-2 file. |
| cifti.stop.if.cifti | Refuse to read a CIFTI file as a volume or morphometry file. |
| cifti.stop.if.cifti.name | Refuse a CIFTI-2 file name for a file that is not a CIFTI-2... |
| cifti.structure.canonical | Normalize a CIFTI brain structure name. |
| cifti.structure.data | Extract the data of one brain structure from a CIFTI-2 file. |
| cifti.structure.data.dim | Get the matrix dimension a brain structure lives in. |
| cifti.structure.data.one | Extract the data of one brain structure (internal). |
| cifti.structure.from.specifier | Resolve a user-supplied structure specifier to a canonical... |
| cifti.structures | Get the brain model table of a CIFTI-2 file. |
| cifti.structure.short | Get the short name of a CIFTI brain structure. |
| cifti.subset.dim | Subset one dimension of an array. |
| cifti.surface.vertex.count | Get the number of vertices of one surface of a CIFTI-2... |
| cifti.surface.vertex.counts | Get the number of vertices of the surfaces declared in a... |
| cifti.validate.axes | Validate the axes of a CIFTI-2 file. |
| cifti.validate.brain.models | Validate the brain model entries of a CIFTI mapping. |
| cifti.validate.dims.coverage | Check that all matrix dimensions are described exactly once. |
| cifti.validate.file.extension | Check the file extension against the axes of the data. |
| cifti.validate.index.range | Check that all indices are within a valid range. |
| cifti.validate.indices.map | Validate a parsed CIFTI MatrixIndicesMap. |
| cifti.validate.parcels | Validate the parcels of a CIFTI mapping. |
| cifti.validate.read.size | Check the safety limit for reading a CIFTI-2 data matrix. |
| cifti.volume | Create a CIFTI-2 axis for a volume. |
| cifti.xml.add.indices.map | Add a MatrixIndicesMap element to the Matrix element. |
| cifti.xml.add.metadata | Add a MetaData element to an XML node. |
| cifti.xml.int.vector | Format an integer vector for an XML text node. |
| cifti.xml.num | Format a number like the reference implementations do. |
| cifti.xml.num.vector | Format a numeric vector for an XML text node. |
| cifti.xml.version | The CIFTI version this package writes. |
| closest.vert.to.point | Find vertex index closest to given query coordinate using... |
| colortable.from.annot | Extract color lookup table (LUT) from annotation. |
| coord.bbox | Compute the bounding box of a set of coordinates. |
| coord.to.key | Turn coordinate vector into string. |
| delete_all_opt_data | Delete all data in the package cache. |
| detect.dti.tract.format | Detect the format of a DTI tract file. |
| doapply.transform.mtx | Apply a spatial transformation matrix to the given... |
| dot-canonicalize.gradient.table | Bring a gradient table into the canonical 'one row per... |
| dot-cifti.label.table.for.users | Convert a label table to the format the package has always... |
| dot-dti.bzero.threshold | Get the b-value threshold below which a volume counts as a... |
| dot-find.bval.file | Find the b-value file that belongs to a b-vector file. |
| dot-format.gradient.values | Format numeric values for a gradient table text file. |
| dot-format.header.size | Format a possibly missing TRK header size for an error... |
| dot-name.gradient.table.columns | Name the columns of an MRtrix gradient table. |
| dot-read.dti.tcktsf | Read DTI tracking data from MRtrix TCK and TSF files. |
| dot-read.numeric.table | Read a whitespace-separated numeric table from a text file. |
| dot-write.numeric.table | Write a numeric table to a text file, one matrix row per... |
| 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. |
| euclidian.dist | Compute Euclidean distance. |
| 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. |
| fileopen.gz.or.not | Get connection to a binary file, gz or not. |
| fileopen.write.gz.or.not | Open a connection for writing, with gzip support based on the... |
| filepath.ends.with | Check whether filepath ends with extension. |
| finite.rows | Check which rows of a matrix consist of finite values only. |
| fixed.vec.format.int | Write fixed width integers to one or several lines. |
| flip2D | Flip a 2D matrix. |
| flip3D | Flip a 3D array along an axis. |
| format_bytes_human | Format a number of bytes for human consumption. |
| fread3 | Read 3-byte integer. |
| 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 |
| fsl.scaled.voxel.matrix | Compute the matrix that maps FSL voxel coordinates of a... |
| 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... |
| fs.tracts.coords | Get the concatenated coordinates of fs.tracts instances. |
| fs.tracts.count | Get the number of tracts. |
| fs.tracts.lengths | Get the number of points of each tract. |
| fs.tracts.point.count | Get the total number of points of all tracts. |
| fs.transform | Create an fs.transform instance. |
| fwrite3 | Write 3-byte integer. |
| get.dti.trk.endianness | Determine endianness of TRK file. |
| get_max_alloc_bytes | Get the configured maximum allocation size in bytes. |
| get_opt_data_filepath | Access a single file from the package cache by its file name. |
| get.slice.orientation | Compute MGH orientation string and direction |
| 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. |
| giftixml_add_labeltable_from_annot | Add a label tabel from an annotation to a GIFTI XML tree. |
| giftixml_add_labeltable_posneg | Add a standard label tabel for to a GIFTI XML tree. |
| gifti_xml_write | Write XML tree to a gifti file. |
| groups.in.bbox | Check which groups have at least one point inside a box. |
| group.start.rows | Compute the first row of every group in a concatenated... |
| guess.filename.is.gzipped | Guess whether a file is gzipped. |
| guess.transform.format | Determine the format of a transformation file. |
| guess.writable.transform.format | Determine the format of a transformation file to write. |
| has_pandoc | Check for pandoc availability on system. |
| infinite.rows | Check which rows of a matrix consist of infinite values only. |
| int.to.col.brainvoyager | Convert 32 bit integer to RGB color as described in... |
| invert.fs.transform | Invert a transformation. |
| inv.ornt.aff | Build the affine that undoes an orientation transform. |
| io.orientation | Determine the orientation of an affine's input axes. |
| 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.gzip.file | Check whether a file is gzip-compressed, based on its magic... |
| is.identity.matrix | Check whether a matrix is (close to) the identity. |
| is.mghheader | Check whether object is an mghheader |
| is.mrtrix.end.line | Check whether a header line terminates the MRtrix header. |
| itk.key.value | Read the value of a key of an ITK transform file. |
| itk.numeric.value | Read a numerical entry of an ITK transform file. |
| length.fs.tracts | Number of tracts in an fs.tracts instance. |
| linesplit.fixed | Split a string into fixed-length parts. |
| list_opt_data | Get file names available in package cache. |
| lta.volume.info.lines | Write the volume info section of an LTA file. |
| m44_to_quaternion | Compute quaternion representation of a rotation from a 4x4... |
| merge.bbox | Merge two bounding boxes. |
| mesh.face.normals | Compute the normals of the triangles of a mesh. |
| mghheader | Constructor to init MGH header instance. |
| 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... |
| mghheader.tkreg2scanner | Compute tkreg-RAS to scanner-RAS matrix from basic MGH header... |
| 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. |
| mgh.is.conformed | Determine whether an MGH volume is conformed. |
| mni152reg | Get fsaverage (MNI305) to MNI152 transformation matrix. |
| mri_dtype_numbytes | Get size of MRI dtype in bytes. |
| mrtrix.track.iterator | Create an iterator over the tracts of an MRtrix TCK or TSF... |
| next.buffer.capacity | Compute the next capacity for a growing result buffer. |
| 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... |
| 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... |
| nifti2.extension | Create a NIFTI v2 header extension. |
| nifti2.extension.content | Get the payload of a NIFTI v2 header extension as raw bytes. |
| nifti2.extension.size | Compute the size of a NIFTI v2 header extension in a file. |
| 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. |
| nifti2.read.extensions | Read the header extensions of a NIFTI v2 file. |
| nifti2.strip.nul | Remove NUL bytes from a raw vector. |
| nifti2.trailing.nul.removed | Remove trailing NUL bytes from a raw vector. |
| nifti2.write.extensions | Write the header extensions of a NIFTI v2 file. |
| nifti.datadim.from.dimfield | Compute data dimensions from the 'dim' field of the NIFTI (v1... |
| nifti.datadim.to.dimfield | Compute NIFTI dim field for data dimension. |
| nifti.dtypebitpix.info.from.mgh.dtype | Compute the 'datatype' and 'bitpix' fields used in the NIFTI1... |
| nifti.dtype.info | Compute NIFTI v1 data type info from datatype and bitpix... |
| nifti.field.check.length | Check whether vector has expected length. |
| nifti.field.check.nchar.max | Check whether character string fields have less than or equal... |
| 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... |
| nifti.header.check | Perform basic sanity checks on NIFTI header data. These are... |
| nifti.header.to.vox2ras | Compute the voxel-to-RAS matrix from the geometry fields of a... |
| nifti.info.from.file | Read the header information and the data of a NIFTI file into... |
| nifti.info.from.oro.instance | Extract the header information and the data of an 'oro.nifti'... |
| nifti.resolve.filepath | Resolve the path of a NIFTI file which is given without a... |
| nifti.space.info | Compute NIFTI space unit info from xyzt_units header field. |
| nifti.time.info | Compute NIFTI time unit info from xyzt_units header field. |
| nifti.transform.type.name | Get the name of the transform type from a form code. |
| nii1header.for.mgh | Create a NIFTI v1 header from the header information... |
| nrrd.dwi.info | Parse the diffusion metadata of a NRRD header. |
| nrrd.field | Look up a field in a parsed NRRD header. |
| nrrd.field.key | Parse a NRRD header field name into a lookup key. |
| nrrd.parse.field.value | Parse a NRRD header field value. |
| nrrd.parse.header | Parse the header lines of a NRRD file. |
| nrrd.parse.matrix | Parse a NRRD matrix value like '(1,0,0) (0,1,0) (0,0,1)'. |
| nrrd.parse.quoted.list | Parse a quoted NRRD string list. |
| nrrd.parse.vector | Parse a NRRD vector value like '(1,2,3)'. |
| nrrd.parse.vector.list | Parse a NRRD vector list value like '(1,0,0) (0,1,0)... |
| nrrd.raw.to.numeric | Convert raw bytes of wide integer types into numbers. |
| nrrd.read.data | Read the data section of a NRRD file. |
| nrrd.read.header.lines | Read the ASCII header of a NRRD file. |
| nrrd.read.remainder | Read the remaining bytes of a connection. |
| nrrd.read.values | Read NRRD values from a connection or a file. |
| nrrd.resolve.data.files | Resolve the data location of a NRRD file. |
| nrrd.skip.lines | Skip whole lines of a connection. |
| nrrd.type.info | Convert the NRRD type name of a volume into R data type... |
| nrrd.vox2ras | Compute the voxel-to-RAS matrix of a NRRD volume. |
| open.maybe.gzip | Open a connection that transparently handles gzip... |
| open.mrtrix.payload | Open the payload of an MRtrix TCK/TSF file for reading. |
| ornt2axcodes | Convert an orientation array to axis codes. |
| ornt.transform | Determine the orientation transform between two orientations. |
| parse.mrtrix.count | Parse the 'count' entry of an MRtrix TCK/TSF header. |
| parse.mrtrix.datatype | Validate and describe the datatype entry of an MRtrix TCK/TSF... |
| parse.mrtrix.file.entry | Parse the 'file' entry of an MRtrix TCK/TSF header. |
| parse.mrtrix.header | Parse the key-value pairs of an MRtrix TCK/TSF header. |
| parse.mrtrix.write.datatype | Parse and validate the datatype of an MRtrix streamlines... |
| parse.stl.ascii.face | Parse a single ASCII STL face. |
| parse.transform.matrix.lines | Parse matrix from text file lines. |
| ply.header.lines | Generate PLY format header lines |
| polygon.soup.to.indexed.mesh | Turn polygon soup into indexed mesh. |
| 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... |
| ras.to.talairachras | Compute MNI talairach coordinates from RAS coords. |
| readable.files | Find files with the given base name and extensions that... |
| 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... |
| readcolortable | Read binary colortable in v2 format. |
| readcolortable_oldformat | Read binary colortable in old format. |
| 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'... |
| read.dti.tsf.header | Read the header of a file in MRtrix 'TSF' format. |
| read.element.counts.ply.header | Determine element counts from PLY file header. |
| read.fixed.char.binary | Read fixed length char, possibly containing embedded zeroes,... |
| 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... |
| 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,... |
| 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... |
| 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... |
| read.fs.surface.stl.ascii | Read surface mesh in STL ASCII format. |
| 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... |
| 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... |
| 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.fs.weight.asc | Read ASCII version of FreeSurfer weight file. |
| read.matlab.v4.matrix | Read the matrices of a MATLAB v4 data file. |
| read.mesh.brainvoyager | Read Brainvoyager srf format (.srf) mesh. |
| read.mrtrix.header | Read the ASCII header of an MRtrix TCK/TSF file. |
| read.mrtrix.stream | Read the data payload of an MRtrix TCK/TSF file. |
| read.nifti1.data | Read raw NIFTI v1 data from file (which may contain the... |
| read.nifti1.header | Read NIFTI v1 header from file (which may contain the... |
| read.nifti1.header.internal | Read NIFTI v1 header from file (which may contain the... |
| read.nifti2.data | Read raw data from NIFTI v2 file. |
| read.nifti2.header | Read NIFTI v2 header from file. |
| read.nifti2.header.internal | Read NIFTI v2 header from file. |
| read.nifti.values | Read raw voxel values of a NIFTI v1/v2 or ANALYZE file from a... |
| 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. |
| read.nrrd.header | Read the header of a file in NRRD format. |
| read_safe_bin | Safe wrapper around readBin that verifies the number of... |
| read.smp.brainvoyager | Read Brainvoyager statistical surface results from SMP file. |
| read.smp.brainvoyager.v1or2 | Read Brainvoyager statistical surface results from v1 or v2... |
| read.smp.brainvoyager.v3 | Read Brainvoyager statistical surface results from v3 SMP... |
| read.smp.brainvoyager.v4or5 | Read Brainvoyager statistical surface results from v4 or v5... |
| read.trk.records | Read the track records of a TRK file. |
| read.vtk.legacy.polydata | Read a VTK legacy file with a POLYDATA dataset. |
| rotate2D | Rotate a 2D matrix in 90 degree steps. |
| rotate3D | Rotate a 3D array in 90 degree steps. |
| rotate90 | Rotate 2D matrix clockwise in 90 degree steps. |
| scan.dti.tract.file | Scan a tract file without holding its data in memory. |
| scan.mrtrix.file | Scan an MRtrix TCK or TSF file. |
| scann | Scan exactly n values from source string. |
| scan.trk.file | Scan a TRK file. |
| skip.connection.bytes | Skip over bytes of a connection, transparently handling gzip. |
| sm0to1 | Adapt spatial transformation matrix for 1-based indices. |
| sm1to0 | Adapt spatial transformation matrix for 0-based indices. |
| split.mrtrix.chunk | Split one chunk of MRtrix payload values into streamlines. |
| stl.format.file.is.ascii | Guess whether a mesh file in STL format is the ASCII or the... |
| sub-.fs.tracts | Subset an fs.tracts instance. |
| subset.groups | Extract selected groups from a concatenated matrix. |
| sub-sub-.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... |
| surfaceras.to.talairach | Compute Talairach RAS for surface RAS (e.g., vertex... |
| talairachras.to.ras | Compute MNI talairach coordinates from RAS coords. |
| text.line.is.numeric | Check whether a text line holds a fixed number of numerical... |
| trackvis.affine.to.rasmm | Compute the affine that maps TrackVis coordinates to RAS+ mm. |
| 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. |
| transform.bbox | Transform a bounding box with an affine. |
| transform.descriptor.path | Get the file path recorded in a volume descriptor. |
| transform.file.sniff.text | Extract the text of a file for format sniffing. |
| transform.flip.handedness | Convert a transformation between the LPS and the RAS... |
| transform.geometry.for.side | Determine the volume geometry of one side of a... |
| transform.matrix.row.lines | Format the rows of a transformation matrix for a text file. |
| transform.values.text | Format numerical values for a transformation text file. |
| transform.value.text | Format a single numerical value for a transformation text... |
| transform.world.frame | Determine the frame of the world space of a transformation. |
| translate.mri.dtype | Translate between code and name of MRI data types. |
| trk.track.iterator | Create an iterator over the tracts of a TRK file. |
| validate_allocation_size | Validate that a requested allocation does not exceed the... |
| validate.bbox | Validate a bounding box argument. |
| validate.dti.gradients | Validate and normalize a diffusion MRI gradient table. |
| validate.fs.transform | Check whether an object is a valid fs.transform instance. |
| vertexdists.to.point | Compute Euclidean distance from all mesh vertices to given... |
| vertex.euclid.dist | Compute Euclidean distance between two vertices v1 and v2. |
| volume.descriptor | Describe a volume for an fs.transform. |
| volume.geometry | Get the geometry of a volume. |
| vtk.as.indices | Convert values that are used as indices to integers. |
| vtk.cell.section.layout | Determine how the cell array of a section is stored. |
| vtk.check.triangles | Check that all cells of the requested type are triangles. |
| vtk.data.type.info | Get the on-disk properties of a VTK legacy data type. |
| vtk.next.line | Read the next line of an ASCII VTK legacy file. |
| vtk.next.section | Read the next section header line of a VTK legacy file. |
| vtk.parse.cell.section | Read the cell array of a VTK legacy section. |
| vtk.parse.count | Read a non-negative integer from a VTK section header. |
| vtk.peek.line | Look at the next line of an ASCII VTK legacy file. |
| vtk.reader.bytes | Consume bytes from a VTK legacy reader. |
| vtk.reader.close | Close the connection of a VTK legacy reader. |
| vtk.reader.fill | Fill the lookahead buffer of a VTK legacy reader. |
| vtk.reader.new | Create the low-level state used while reading a VTK legacy... |
| vtk.reader.numbers | Read numeric values from a binary VTK legacy file. |
| vtk.reader.peek | Read bytes from a VTK legacy reader without consuming them. |
| vtk.read.header | Read the header of a VTK legacy file and set up the reader. |
| vtk.section.values | Read numeric values from a VTK legacy section. |
| vtk.section.values.ascii | Read numeric values from an ASCII VTK legacy section. |
| vtk.split.line | Split a line of a VTK legacy file into whitespace separated... |
| vtk.write.surface.ascii | Write the sections of a triangular mesh in VTK ASCII format. |
| vtk.write.surface.binary | Write the sections of a triangular mesh in binary VTK format. |
| write.analyze | Write data to a file in ANALYZE 7.5 format. |
| write.analyze.char.field | Write a fixed length character field of an ANALYZE 7.5... |
| write.analyze.header.internal | Write the 348 byte ANALYZE 7.5 header to a connection. |
| write.atlas.to.lut.and.csv | Write a brain atlas to a colortable (LUT) file and a... |
| 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... |
| 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.off.ply2 | Write mesh to file in Object File Format (.off) or PLY2... |
| 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... |
| write.fs.weight | Write file in FreeSurfer weight format |
| write.fs.weight.asc | Write file in FreeSurfer weight ASCII format |
| write.mrtrix.streamlines | Write the payload of an MRtrix streamlines file. |
| write.nifti1 | Write header and data to a file in NIFTI v1 format. |
| write.nifti1.data.internal | Write the voxel data of a NIFTI v1 file to a connection. |
| write.nifti1.header.internal | Write the 348 byte NIFTI v1 header (and the padding up to the... |
| write.nifti2 | Write header and data to a file in NIFTI v2 format. |
| write.smp.brainvoyager | Write a brainvoyager SMP file. |
| write.smp.brainvoyager.v2 | Write a brainvoyager v2 SMP file. |
| write.smp.brainvoyager.v3or4or5 | Write a brainvoyager v3, v4 or v5 SMP file. |
| write.stl.ascii | Write the sections of a triangular mesh in ASCII STL format. |
| write.stl.binary | Write the sections of a triangular mesh in binary STL format. |
| write.trk.header | Write the 1000 byte header of a TRK file. |
| xml_node_gifti_coordtransform | Create XML GIFTI CoordinateSystemTransformMatrix node. |
| xml_node_gifti_label | Create XML GIFTI Label node. |
| xml_node_gifti_label_table | Create XML GIFTI LabelTable node. |
| xml_node_gifti_label_table_from_annot | Compute LabelTable node from annotation. |
| xml_node_gifti_MD | Create XML GIFTI metadata node. |
