| adjust.face.indices.to | Adjust integer matrix to target min value. |
| annot.max.region.idx | Get max region index of an fs.annot instance. |
| annot.unique | Make the region names and indices unique across hemispheres... |
| assert.surface | Stop unless surf is an fs.surface |
| bvsmp | Create new bvsmp instance encoding morph data for... |
| cdata | Create CDATA element string from string. |
| 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. |
| closest.vert.to.point | Find vertex index closest to given query coordinate using... |
| colortable.from.annot | Extract color lookup table (LUT) from annotation. |
| coord.to.key | Turn coordinate vector into string. |
| delete_all_opt_data | Delete all data in the package cache. |
| doapply.transform.mtx | Apply a spatial transformation matrix to the given... |
| download_opt_data | Download optional data for the freesurferformats package. |
| 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. |
| filepath.ends.with | Check whether filepath ends with extension. |
| 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. |
| 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 |
| fs.patch | Constructor for fs.patch |
| fs.surface.to.tmesh3d | Get an rgl tmesh3d instance from a brain surface mesh. |
| fwrite3 | Write 3-byte integer. |
| get.dti.trk.endianness | Determine endianness of TRK file. |
| 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. |
| guess.filename.is.gzipped | Guess whether a file is gzipped. |
| has_pandoc | Check for pandoc availability on system. |
| int.to.col.brainvoyager | Convert 32 bit integer to RGB color as described in... |
| is.bvsmp | Check whether object is a bvsmp instance. |
| is.fs.annot | Check whether object is an fs.annot |
| is.fs.label | Check whether object is an fs.label |
| is.fs.surface | Check whether object is an fs.surface |
| is.fs.volume | Check whether object is an fs.volume |
| is.mghheader | Check whether object is an mghheader |
| linesplit.fixed | Split a string into fixed-length parts. |
| list_opt_data | Get file names available in package cache. |
| 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. |
| 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... |
| 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.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.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. |
| 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.fs.annot | Print description of a brain atlas or annotation. |
| print.fs.label | Print description of a brain surface label. |
| print.fs.patch | Print description of a brain surface patch. |
| print.fs.surface | Print description of a brain surface. |
| print.fs.volume | Print description of a brain volume. |
| 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... |
| readcolortable | Read binary colortable in v2 format. |
| readcolortable_oldformat | Read binary colortable in old format. |
| read.dti.tck | Read DTI tracking data from file in MRtrix 'TCK' format. |
| read.dti.trk | Read fiber tracks from Diffusion Toolkit in trk format. |
| read.dti.tsf | Read DTI tracking per-coord data from file in MRtrix 'TSF'... |
| 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.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.patch | Read FreeSurfer binary or ASCII patch file. |
| read.fs.patch.asc | Read FreeSurfer ASCII format patch. |
| read.fs.surface | Read file in FreeSurfer surface format or various mesh... |
| 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 ASCII format mesh as surface. |
| read.fs.transform | Load transformation matrix from a file. |
| read.fs.transform.dat | Load transformation matrix from a tkregister dat file. |
| read.fs.transform.lta | Load transformation matrix from a FreeSurfer linear transform... |
| read.fs.transform.xfm | Load transformation matrix from an XFM file. |
| read.fs.volume | Read volume file in MGH, MGZ or NIFTI format |
| read.fs.volume.nii | Turn a 3D or 4D 'oro.nifti' instance into an 'fs.volume'... |
| read.fs.weight | Read file in FreeSurfer weight or w format |
| read.fs.weight.asc | Read ASCII version of FreeSurfer weight file. |
| read.mesh.brainvoyager | Read Brainvoyager srf format (.srf) mesh. |
| 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_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.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... |
| 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. |
| scann | Scan exactly n values from source string. |
| sm0to1 | Adapt spatial transformation matrix for 1-based indices. |
| sm1to0 | Adapt spatial transformation matrix for 0-based indices. |
| stl.format.file.is.ascii | Guess whether a mesh file in STL format is the ASCII or the... |
| 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. |
| translate.mri.dtype | Translate between code and name of MRI data types. |
| vertexdists.to.point | Compute Euclidean distance from all mesh vertices to given... |
| vertex.euclid.dist | Compute Euclidean distance between two vertices v1 and v2. |
| write.fs.annot | Write annotation to binary file. |
| write.fs.annot.gii | Write annotation to GIFTI file. |
| write.fs.colortable | Write colortable file in FreeSurfer ASCII LUT format. |
| write.fs.curv | Write file in FreeSurfer curv format |
| write.fs.label | Write vertex indices to file in FreeSurfer label format |
| write.fs.label.gii | Write a binary surface label in GIFTI format. |
| write.fs.mgh | Write file in FreeSurfer MGH or MGZ format |
| write.fs.morph | Write morphometry data in a format derived from the given... |
| write.fs.morph.asc | Write file in FreeSurfer ASCII curv format |
| write.fs.morph.gii | Write morphometry data in GIFTI format. |
| write.fs.morph.ni1 | Write morphometry data in NIFTI v1 format. |
| write.fs.morph.ni2 | Write morphometry data in NIFTI v2 format. |
| write.fs.morph.smp | Write morphometry data in Brainvoyager SMP format. |
| write.fs.morph.txt | Write curv data to file in simple text format |
| write.fs.patch | Write a surface patch |
| write.fs.surface | Write mesh to file in FreeSurfer binary surface format |
| write.fs.surface.asc | Write mesh to file in FreeSurfer ASCII surface format |
| write.fs.surface.bvsrf | Write surface to Brainvoyager SRF file. |
| write.fs.surface.byu | Write mesh to file in BYU ASCII format. |
| write.fs.surface.gii | Write mesh to file in GIFTI surface format |
| write.fs.surface.mz3 | Write mesh to file in mz3 binary format. |
| write.fs.surface.obj | Write mesh to file in Wavefront object (.obj) format |
| write.fs.surface.off | Write mesh to file in Object File Format (.off) |
| write.fs.surface.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.vtk | Write mesh to file in VTK ASCII format |
| write.fs.weight | Write file in FreeSurfer weight format |
| write.fs.weight.asc | Write file in FreeSurfer weight ASCII format |
| write.nifti1 | Write header and data to a file in NIFTI v1 format. |
| write.nifti2 | Write header and data to a file in NIFTI v2 format. |
| write.smp.brainvoyager | Write a brainvoyager SMP file. |
| write.smp.brainvoyager.v2 | Write a brainvoyager v2 SMP file. |
| write.smp.brainvoyager.v3or4or5 | Write a brainvoyager v3, v4 or v5 SMP 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. |
