Read 3-byte integer.
fs.get.morph.file.ext.for.format
Determine morphometry file extension from format
Delete all data in the package cache.
Convert tris faces to quad faces by simple merging.
Turn coordinate vector into string.
fs.get.morph.file.format.from.filename
Determine morphometry file format from filename
Check whether object is an fs.label
Constructor for fs.patch
Get GIFTI XML representation of data.
gifti_xml_add_global_metadata
Add metadata to GIFTI XML tree.
Get connection to a binary file, gz or not.
Write data to a gifti file.
Access a single file from the package cache by its file name.
Check whether object is a bvsmp instance.
mghheader.centervoxelRAS.from.firstvoxelRAS
Compute RAS coords of center voxel.
Constructor to init MGH header instance.
Determine whether an MGH volume is conformed.
Compute MGH orientation string and direction
Convert 32 bit integer to RGB color as described in Brainvoyager SRF file spec.
Check for pandoc availability on system.
Check whether object is an fs.surface
Convert quadrangular faces or polygons to triangular ones.
Check whether object is an fs.annot
Determine endianness of TRK file.
mghheader.crs.orientation
Compute MGH volume orientation string.
Compute ras2vox-tkreg matrix from basic MGH header fields.
Check whether header contains valid ras information
Create a template NIFTI v1 header. You will have to adapt it for your use case.
Determine whether an MGH volume is conformed.
Determine NIFTI file version information and whether file is a NIFTI file.
Determine whether a NIFTI file uses the FreeSurfer hack.
guess.filename.is.gzipped
Guess whether a file is gzipped.
Print description of a brain surface patch.
Check whether object is an fs.volume
Flip a 2D matrix.
Flip a 3D array along an axis.
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.
Read file in FreeSurfer curv format
Read colortable file in FreeSurfer ASCII LUT format.
Print description of a brain surface.
Read file in FreeSurfer MGH or MGZ format
Read morphometry data file in any FreeSurfer format.
giftixml_add_labeltable_posneg
Add a standard label tabel for to a GIFTI XML tree.
Check whether object is an mghheader
mghheader.primary.slice.direction
Compute MGH primary slice direction
Compute ras2vox matrix from basic MGH header fields.
Get an rgl tmesh3d instance from a brain surface mesh.
Compute vox2ras matrix from basic MGH header fields.
Read file in FreeSurfer annotation format
Read FreeSurfer GCA file.
Read FreeSurfer binary or ASCII patch file.
read.fs.surface.stl.ascii
Read surface mesh in STL ASCII format.
Read FreeSurfer ASCII format patch.
Create NIFTI v2 header suitable for given data.
Read an annotation or label in GIFTI format.
Read a label file.
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.
Read GEO format mesh as surface.
Compute vox2ras-tkreg matrix from basic MGH header fields.
Read surface mesh in STL binary format.
Write 3-byte integer.
nifti.datadim.to.dimfield
Compute NIFTI dim field for data dimension.
Load transformation matrix from an XFM file.
read_nisurfacefile.fsascii
Read a FreeSurfer ASCII surface file.
Read volume file in MGH, MGZ or NIFTI format
nifti.field.check.nchar.max
Check whether character string fields have less than or equal to expected length.
Check whether vector has expected length.
read.nifti2.header.internal
Read NIFTI v2 header from file.
Compute scanner-RAS 2 tkreg-RAS matrix from basic MGH header fields.
Read NIFTI v2 header from file.
Write XML tree to a gifti file.
read_nisurfacefile.fsnative
Read a FreeSurfer ASCII surface file.
Parse a single ASCII STL face.
Read VTK ASCII format mesh as surface.
Read a label from a GIFTI label/annotation file.
Read GIFTI format mesh as surface.
Read Brainvoyager srf format (.srf) mesh as surface.
Load transformation matrix from a file.
Read file in FreeSurfer label format
Read mesh in BYU format.
Rotate 2D matrix clockwise in 90 degree steps.
Compute NIFTI v1 data type info from datatype and bitpix header field.
parse.transform.matrix.lines
Parse matrix from text file lines.
Print description of a brain atlas or annotation.
Compute vox2vox matrix between two volumes.
Print description of a brain surface label.
Read Brainvoyager srf format (.srf) mesh.
Read binary colortable in v2 format.
Read ASCII version of FreeSurfer weight file.
Read NIFTI v1 header from file (which may contain the FreeSurfer hack).
Read Brainvoyager statistical surface results from SMP file.
Compute MNI talairach coordinates from RAS coords.
Read raw NIFTI v1 data from file (which may contain the FreeSurfer hack).
read.smp.brainvoyager.v1or2
Read Brainvoyager statistical surface results from v1 or v2 SMP file.
Perform basic sanity checks on NIFTI header data. These are in no way meant to be exhaustive.
Read morphometry data from ASCII curv format file
Read DTI tracking data from file in MRtrix 'TCK' format.
giftixml_add_labeltable_from_annot
Add a label tabel from an annotation to a GIFTI XML tree.
Write a binary surface label in GIFTI format.
Get fsaverage (MNI305) to MNI152 transformation matrix.
Read binary colortable in old format.
Compute NIFTI space unit info from xyzt_units header field.
Scan exactly n values from source string.
Read a surface, based on the file path without extension.
Write annotation to GIFTI file.
Write file in FreeSurfer MGH or MGZ format
S3 method to read a neuroimaging surface file.
Guess whether a mesh file in STL format is the ASCII or the binary version.
Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS.
Write annotation to binary file.
Compute Euclidean distance from all mesh vertices to given point.
Generate PLY format header lines
Compute tkreg-RAS to scanner-RAS matrix from basic MGH header fields.
Split a string into fixed-length parts.
Get file names available in package cache.
mghheader.update.from.vox2ras
Update mghheader fields from vox2ras matrix.
polygon.soup.to.indexed.mesh
Turn polygon soup into indexed mesh.
Write mesh to file in GIFTI surface format
Read fiber tracks from Diffusion Toolkit in trk format.
Write morphometry data in NIFTI v1 format.
Write header and data to a file in NIFTI v1 format.
Write mesh to file in FreeSurfer binary surface format
Write colortable file in FreeSurfer ASCII LUT format.
Write mesh to file in FreeSurfer ASCII surface format
Write morphometry data in GIFTI format.
Write surface to Brainvoyager SRF file.
Write mesh to file in BYU ASCII format.
Write header and data to a file in NIFTI v2 format.
Write mesh to file in Object File Format (.off)
Write mesh to file in Wavefront object (.obj) format
write.smp.brainvoyager.v3or4or5
Write a brainvoyager v3, v4 or v5 SMP file.
Read DTI tracking per-coord data from file in MRtrix 'TSF' format.
Write mesh to file in mz3 binary format.
Read Brainvoyager vertex-wise statistical surface data from SMP file.
Create XML GIFTI Label node.
xml_node_gifti_coordtransform
Create XML GIFTI CoordinateSystemTransformMatrix node.
Read morphometry data from FreeSurfer NIFTI v1 format files.
Read OBJ format mesh as surface.
Read morphometry data from FreeSurfer NIFTI v2 format files.
Load transformation matrix from a tkregister dat file.
Print description of a brain volume.
Read Object File Format (OFF) mesh as surface.
Create NIFTI v1 header suitable for given data.
Translate RAS coordinates, as used in volumes by applying vox2ras, to surface RAS.
Get size of MRI dtype in bytes.
read.element.counts.ply.header
Determine element counts from PLY file header.
Read fixed length char, possibly containing embedded zeroes, from binary file.
Read morphometry data from FreeSurfer NIFTI format files, determine NIFTI version automatically.
Read morphometry data from plain text file
Read morphometry data file in GIFTI format.
Load transformation matrix from a FreeSurfer linear transform array (LTA) file.
Read surface morphometry data from CIFTI dscalar files.
Create XML GIFTI metadata node.
Read file in FreeSurfer surface format or various mesh formats.
Read FreeSurfer ASCII format surface.
Rotate a 2D matrix in 90 degree steps.
Adapt spatial transformation matrix for 1-based indices.
Read Stanford PLY format mesh as surface.
Read file in FreeSurfer weight or w format
Read mesh in STL format, auto-detecting ASCII versus binary format version.
Adapt spatial transformation matrix for 0-based indices.
Read surface mesh in mz3 format, used by Surf-Ice.
Read ICO format mesh as surface.
Rotate a 3D array in 90 degree steps.
Turn a 3D or 4D `oro.nifti` instance into an `fs.volume` instance with complete header.
write.fs.surface.off.ply2
Write mesh to file in Object File Format (.off) or PLY2 format.
Write mesh to file in PLY format (.ply)
Read raw data from NIFTI v2 file.
Find files with the given base name and extensions that exist.
read.nifti1.header.internal
Read NIFTI v1 header from file (which may contain the FreeSurfer hack).
Write file in FreeSurfer curv format
Write vertex indices to file in FreeSurfer label format
Compute Euclidean distance between two vertices v1 and v2.
Write morphometry data in Brainvoyager SMP format.
Write morphometry data in NIFTI v2 format.
Read a gifti file as a surface.
Write mesh to file in PLY2 File Format (.ply2)
Compute Talairach RAS for surface RAS (e.g., vertex coordinates).
Translate between code and name of MRI data types.
Read Brainvoyager statistical surface results from v3 SMP file.
xml_node_gifti_label_table
Create XML GIFTI LabelTable node.
Compute MNI talairach coordinates from RAS coords.
Write a surface patch
Write file in FreeSurfer weight format
Write mesh to file in VTK ASCII format
Write a brainvoyager SMP file.
Write morphometry data in a format derived from the given file name.
Write file in FreeSurfer ASCII curv format
Write curv data to file in simple text format
Write file in FreeSurfer weight ASCII format
xml_node_gifti_label_table_from_annot
Compute LabelTable node from annotation.
read.smp.brainvoyager.v4or5
Read Brainvoyager statistical surface results from v4 or v5 SMP file.
write.smp.brainvoyager.v2
Write a brainvoyager v2 SMP file.
Get max region index of an fs.annot instance.
Create new bvsmp instance encoding morph data for Brainvoyager.
Make the region names and indices unique across hemispheres for a parcellation.
Extract color lookup table (LUT) from annotation.
Find vertex index closest to given query coordinate using Euclidean distance.
Create CDATA element string from string.
Apply a spatial transformation matrix to the given coordinates.
Write fixed width integers to one or several lines.
check_data_and_settings_consistency
Warn about common errors in combining data and datatype.
Adjust integer matrix to target min value.
Check whether filepath ends with extension.
Compute Euclidean distance.
Stop unless surf is an fs.surface
Check whether the dtype is suitable for the data.
Download optional data for the freesurferformats package.