API for freesurferformats
Read and Write 'FreeSurfer' Neuroimaging File Formats

Global functions
.canonicalize.gradient.table Man page Source code
.cifti.brain.structure.index Source code
.cifti.label.table.for.users Man page Source code
.cifti.legacy.label.table Source code
.cifti.legacy.map.name Source code
.cifti.legacy.surface.matrix Source code
.dti.bzero.threshold Man page Source code
.find.bval.file Man page Source code
.format.gradient.values Man page Source code
.format.header.size Man page Source code
.get.cifti Source code
.name.gradient.table.columns Man page Source code
.normalize.cifti.brain.structure Source code
.read.dti.tcktsf Man page Source code
.read.numeric.table Man page Source code
.write.numeric.table Man page Source code
CIFTI_EXTENSION_CODE Man page
[.fs.tracts Man page
[[.fs.tracts Man page
`[.fs.tracts` Source code
`[[.fs.tracts` Source code
adjust.face.indices.to Man page Source code
analyze.dtype.info Man page
analyze.header.check Man page Source code
analyze.header.to.vox2ras Man page
analyze.mat.sidecar.to.vox2ras Man page Source code
analyze.pair.files Man page Source code
analyze.read.char.field Man page Source code
analyze.read.header.internal Man page Source code
analyze.read.magic Man page Source code
analyze.write.data.internal Man page Source code
analyzeheader.for.data Man page Source code
analyzeheader.template Man page Source code
annot.max.region.idx Man page
annot.unique Man page
apply.affine.to.coords Man page Source code
as.fs.tracts Man page Source code
as.list.fs.tracts Man page Source code
as.tsf.scalars Man page Source code
assert.surface Man page
assert_package Source code
atlas.from.lut.and.csv Man page Source code
axcodes2ornt Man page Source code
build.mrtrix.header Man page Source code
build.mrtrix.header.stable Man page Source code
bvsmp Man page Source code
cdata Man page Source code
check.dtype.for.data Man page
check.verts.faces Source code
check_all_finite Man page Source code
check_data_and_settings_consistency Man page Source code
check_file_size Man page Source code
cifti.annot.list Man page Source code
cifti.annot.parcels Man page Source code
cifti.array.with.new.first.dim Man page Source code
cifti.assign.rows Man page Source code
cifti.axes.to.maps Man page
cifti.axis.brain.models Man page Source code
cifti.axis.for.maps Man page Source code
cifti.axis.from.template Man page Source code
cifti.axis.labels Man page Source code
cifti.axis.named.maps Man page Source code
cifti.axis.parcels Man page Source code
cifti.axis.parcels.from.annot Man page Source code
cifti.axis.scalars Man page Source code
cifti.axis.series Man page Source code
cifti.axis.size Man page
cifti.axis.surface.sizes Man page Source code
cifti.axis.surfaces Man page
cifti.brain.model.surface Man page Source code
cifti.brain.model.volume Man page Source code
cifti.brainordinate.dim Man page Source code
cifti.brainordinate.dims Man page Source code
cifti.check.axes Man page Source code
cifti.check.data.for.axes Man page
cifti.check.index.list Man page
cifti.check.index.selection Man page Source code
cifti.check.label.table Man page Source code
cifti.check.object Man page Source code
cifti.compute.index.ranges Man page
cifti.connectome.axes Man page Source code
cifti.data.for.all.vertices Man page Source code
cifti.data.for.connectome Man page Source code
cifti.data.for.grayordinates Man page Source code
cifti.data.object Man page Source code
cifti.data.per.structure Man page Source code
cifti.data.structures Man page Source code
cifti.data.surface.size Man page Source code
cifti.dense.structure.matrix Man page Source code
cifti.dim.labels Man page Source code
cifti.dim.to.front Man page Source code
cifti.file.looks.like.cifti1 Man page Source code
cifti.file.looks.like.cifti2 Man page Source code
cifti.file.type.for.axes Man page Source code
cifti.file.type.for.extension Man page Source code
cifti.file.types Man page Source code
cifti.grayordinates Man page Source code
cifti.grayordinates.for.axes Man page Source code
cifti.grayordinates.for.model Man page Source code
cifti.header.from.axes Man page Source code
cifti.header.of Man page Source code
cifti.index.type.short Man page Source code
cifti.index.types Man page Source code
cifti.is.connectome.axis Man page Source code
cifti.label.table Man page Source code
cifti.label.table.for.writing Man page Source code
cifti.map.for.dim Man page Source code
cifti.map.name Man page Source code
cifti.map.type.description Man page Source code
cifti.matrix.dim.sizes Man page Source code
cifti.merge.axes Man page
cifti.model.types Man page Source code
cifti.nifti.header.for.axes Man page Source code
cifti.other.dim Man page Source code
cifti.parcel Man page Source code
cifti.parcels Man page Source code
cifti.parcels.axis.of Man page Source code
cifti.parse.attr Man page Source code
cifti.parse.brain.models Man page Source code
cifti.parse.child.int.vector Man page Source code
cifti.parse.child.voxel.indices Man page Source code
cifti.parse.indices.map Man page Source code
cifti.parse.int.vector Man page Source code
cifti.parse.label.table Man page Source code
cifti.parse.metadata Man page Source code
cifti.parse.named.maps Man page Source code
cifti.parse.numeric.vector Man page Source code
cifti.parse.parcels Man page Source code
cifti.parse.series Man page Source code
cifti.parse.surfaces Man page Source code
cifti.parse.volumes Man page Source code
cifti.parse.xml Man page Source code
cifti.prepare.surface.data Man page Source code
cifti.read.matrix Man page Source code
cifti.read.rows Man page Source code
cifti.read.values Man page Source code
cifti.region.name.without.hemisphere Man page Source code
cifti.series.info Man page Source code
cifti.stop.if.cifti Man page Source code
cifti.stop.if.cifti.name Man page Source code
cifti.structure.canonical Man page Source code
cifti.structure.data Man page Source code
cifti.structure.data.dim Man page Source code
cifti.structure.data.one Man page Source code
cifti.structure.from.specifier Man page Source code
cifti.structure.short Man page Source code
cifti.structures Man page Source code
cifti.subset.dim Man page Source code
cifti.surface.vertex.count Man page Source code
cifti.surface.vertex.counts Man page Source code
cifti.validate.axes Man page Source code
cifti.validate.brain.models Man page Source code
cifti.validate.dims.coverage Man page Source code
cifti.validate.file.extension Man page Source code
cifti.validate.index.range Man page Source code
cifti.validate.indices.map Man page Source code
cifti.validate.parcels Man page Source code
cifti.validate.read.size Man page Source code
cifti.volume Man page Source code
cifti.xml.add.indices.map Man page
cifti.xml.add.metadata Man page
cifti.xml.int.vector Man page
cifti.xml.num Man page
cifti.xml.num.vector Man page
cifti.xml.version Man page Source code
closest.vert.to.point Man page Source code
colortable.from.annot Man page
coord.bbox Man page Source code
coord.to.key Man page Source code
delete_all_opt_data Man page Source code
detect.dti.tract.format Man page Source code
doapply.transform.mtx Man page Source code
download_opt_data Man page Source code
dti.track.bbox Man page Source code
dti.track.count Man page Source code
dti.track.iterator Man page Source code
euclidian.dist Man page Source code
faces.quad.to.tris Man page Source code
faces.tris.to.quad Man page Source code
fileopen.gz.or.not Man page Source code
fileopen.write.gz.or.not Man page Source code
filepath.ends.with Man page Source code
finite.rows Man page Source code
fixed.format.lines Source code
fixed.vec.format.int Man page Source code
flip2D Man page Source code
flip3D Man page Source code
format_bytes_human Man page Source code
fread3 Man page Source code
fs.get.morph.file.ext.for.format Man page Source code
fs.get.morph.file.format.from.filename Man page Source code
fs.patch Man page Source code
fs.surface.to.tmesh3d Man page Source code
fs.tracts Man page Source code
fs.tracts.coords Man page Source code
fs.tracts.count Man page Source code
fs.tracts.lengths Man page Source code
fs.tracts.point.count Man page Source code
fs.transform Man page Source code
fsl.scaled.voxel.matrix Man page Source code
fwrite3 Man page Source code
get.dti.trk.endianness Man page Source code
get.slice.orientation Man page Source code
get_max_alloc_bytes Man page Source code
get_opt_data_filepath Man page Source code
gifti_writer Man page Source code
gifti_xml Man page Source code
gifti_xml_add_global_metadata Man page Source code
gifti_xml_write Man page Source code
giftixml_add_labeltable_from_annot Man page Source code
giftixml_add_labeltable_posneg Man page Source code
group.start.rows Man page Source code
groups.in.bbox Man page Source code
guess.filename.is.gzipped Man page Source code
guess.transform.format Man page Source code
guess.writable.transform.format Man page Source code
has_pandoc Man page Source code
infinite.rows Man page Source code
int.to.col.brainvoyager Man page Source code
inv.ornt.aff Man page Source code
invert.fs.transform Man page Source code
io.orientation Man page Source code
is.analyze.file Man page Source code
is.bvsmp Man page Source code
is.fs.annot Man page
is.fs.label Man page Source code
is.fs.surface Man page Source code
is.fs.tracts Man page Source code
is.fs.transform Man page Source code
is.fs.volume Man page Source code
is.gzip.file Man page Source code
is.identity.matrix Man page Source code
is.mghheader Man page Source code
is.mrtrix.end.line Man page Source code
itk.key.value Man page Source code
itk.numeric.value Man page Source code
length.fs.tracts Man page Source code
linesplit.fixed Man page Source code
list_opt_data Man page Source code
lta.volume.info.lines Man page Source code
m44_to_quaternion Man page Source code
merge.bbox Man page Source code
mesh.face.normals Man page Source code
mgh.is.conformed Man page Source code
mghheader Man page Source code
mghheader.centervoxelRAS.from.firstvoxelRAS Man page Source code
mghheader.crs.orientation Man page Source code
mghheader.is.conformed Man page Source code
mghheader.is.ras.valid Man page Source code
mghheader.primary.slice.direction Man page Source code
mghheader.ras2vox Man page Source code
mghheader.ras2vox.tkreg Man page Source code
mghheader.scanner2tkreg Man page Source code
mghheader.tkreg2scanner Man page Source code
mghheader.update.from.vox2ras Man page Source code
mghheader.vox2ras Man page Source code
mghheader.vox2ras.tkreg Man page Source code
mghheader.vox2vox Man page Source code
mni152reg Man page Source code
mri_dtype_numbytes Man page
mrtrix.track.iterator Man page Source code
next.buffer.capacity Man page Source code
ni1header.for.data Man page
ni1header.template Man page Source code
ni2header.for.data Man page Source code
ni2header.template Man page Source code
nifti.datadim.from.dimfield Man page Source code
nifti.datadim.to.dimfield Man page Source code
nifti.dtype.info Man page Source code
nifti.dtypebitpix.info.from.mgh.dtype Man page Source code
nifti.field.check.length Man page Source code
nifti.field.check.nchar.max Man page Source code
nifti.file.uses.fshack Man page Source code
nifti.file.version Man page Source code
nifti.header.check Man page Source code
nifti.header.to.vox2ras Man page Source code
nifti.info.from.file Man page Source code
nifti.info.from.oro.instance Man page Source code
nifti.resolve.filepath Man page Source code
nifti.space.info Man page Source code
nifti.time.info Man page Source code
nifti.transform.type.name Man page Source code
nifti2.extension Man page Source code
nifti2.extension.content Man page Source code
nifti2.extension.size Man page Source code
nifti2.extension.text Man page Source code
nifti2.get.extension Man page Source code
nifti2.read.extensions Man page Source code
nifti2.strip.nul Man page Source code
nifti2.trailing.nul.removed Man page Source code
nifti2.write.extensions Man page Source code
nii1header.for.mgh Man page Source code
nrrd.dwi.info Man page Source code
nrrd.field Man page Source code
nrrd.field.key Man page Source code
nrrd.parse.field.value Man page Source code
nrrd.parse.header Man page Source code
nrrd.parse.matrix Man page Source code
nrrd.parse.quoted.list Man page Source code
nrrd.parse.vector Man page Source code
nrrd.parse.vector.list Man page Source code
nrrd.raw.to.numeric Man page Source code
nrrd.read.data Man page Source code
nrrd.read.header.lines Man page Source code
nrrd.read.remainder Man page Source code
nrrd.read.values Man page Source code
nrrd.resolve.data.files Man page Source code
nrrd.skip.lines Man page Source code
nrrd.type.info Man page Source code
nrrd.vox2ras Man page Source code
open.maybe.gzip Man page Source code
open.mrtrix.payload Man page Source code
ornt.transform Man page Source code
ornt2axcodes Man page Source code
parse.mrtrix.count Man page Source code
parse.mrtrix.datatype Man page Source code
parse.mrtrix.file.entry Man page Source code
parse.mrtrix.header Man page Source code
parse.mrtrix.write.datatype Man page Source code
parse.stl.ascii.face Man page Source code
parse.transform.matrix.lines Man page Source code
ply.header.lines Man page Source code
polygon.soup.to.indexed.mesh Man page Source code
print.dti.track.iterator Man page Source code
print.fs.annot Man page
print.fs.cifti Man page Source code
print.fs.cifti.data Man page Source code
print.fs.connectome Man page Source code
print.fs.label Man page Source code
print.fs.patch Man page Source code
print.fs.surface Man page Source code
print.fs.tracts Man page Source code
print.fs.transform Man page Source code
print.fs.volume Man page Source code
ras.to.surfaceras Man page Source code
ras.to.talairachras Man page Source code
read.analyze.data Man page
read.analyze.header Man page Source code
read.cifti Man page Source code
read.cifti.header Man page Source code
read.cifti.rows Man page Source code
read.dti.bval Man page Source code
read.dti.bvec Man page Source code
read.dti.grad Man page Source code
read.dti.gradients Man page Source code
read.dti.tck Man page Source code
read.dti.tck.header Man page Source code
read.dti.trk Man page Source code
read.dti.trk.header Man page Source code
read.dti.tsf Man page Source code
read.dti.tsf.header Man page Source code
read.element.counts.ply.header Man page Source code
read.fixed.char.binary Man page Source code
read.fs.annot Man page Source code
read.fs.annot.gii Man page
read.fs.colortable Man page
read.fs.connectome.cifti Man page Source code
read.fs.curv Man page Source code
read.fs.gca Man page
read.fs.label Man page Source code
read.fs.label.gii Man page Source code
read.fs.label.native Man page Source code
read.fs.mgh Man page Source code
read.fs.morph Man page Source code
read.fs.morph.asc Man page Source code
read.fs.morph.bvsmp Man page Source code
read.fs.morph.cifti Man page Source code
read.fs.morph.gii Man page Source code
read.fs.morph.ni1 Man page Source code
read.fs.morph.ni2 Man page Source code
read.fs.morph.nii Man page Source code
read.fs.morph.txt Man page Source code
read.fs.parcellation.cifti Man page Source code
read.fs.patch Man page Source code
read.fs.patch.asc Man page Source code
read.fs.series.cifti Man page Source code
read.fs.surface Man page Source code
read.fs.surface.asc Man page Source code
read.fs.surface.bvsrf Man page Source code
read.fs.surface.byu Man page Source code
read.fs.surface.geo Man page Source code
read.fs.surface.gii Man page Source code
read.fs.surface.ico Man page Source code
read.fs.surface.mz3 Man page Source code
read.fs.surface.obj Man page Source code
read.fs.surface.off Man page Source code
read.fs.surface.ply Man page Source code
read.fs.surface.stl Man page Source code
read.fs.surface.stl.ascii Man page Source code
read.fs.surface.stl.bin Man page Source code
read.fs.surface.vtk Man page Source code
read.fs.tracts.vtk Man page Source code
read.fs.transform Man page Source code
read.fs.transform.dat Man page Source code
read.fs.transform.fslmat Man page Source code
read.fs.transform.itk Man page Source code
read.fs.transform.lta Man page Source code
read.fs.transform.xfm Man page Source code
read.fs.volume Man page Source code
read.fs.volume.analyze Man page
read.fs.volume.nii Man page Source code
read.fs.volume.nrrd Man page Source code
read.fs.weight Man page Source code
read.fs.weight.asc Man page Source code
read.matlab.v4.matrix Man page Source code
read.mesh.brainvoyager Man page Source code
read.mrtrix.header Man page Source code
read.mrtrix.stream Man page Source code
read.nifti.values Man page
read.nifti1.data Man page Source code
read.nifti1.header Man page Source code
read.nifti1.header.internal Man page Source code
read.nifti2.data Man page Source code
read.nifti2.header Man page Source code
read.nifti2.header.internal Man page Source code
read.nrrd.header Man page Source code
read.smp.brainvoyager Man page Source code
read.smp.brainvoyager.v1or2 Man page Source code
read.smp.brainvoyager.v3 Man page Source code
read.smp.brainvoyager.v4or5 Man page Source code
read.trk.records Man page Source code
read.vtk.legacy.polydata Man page Source code
read_nisurface Man page Source code
read_nisurfacefile Man page Source code
read_nisurfacefile.default Source code
read_nisurfacefile.fsascii Man page Source code
read_nisurfacefile.fsnative Man page Source code
read_nisurfacefile.gifti Man page Source code
read_safe_bin Man page Source code
readable.files Man page Source code
readcolortable Man page
readcolortable_oldformat Man page
rotate2D Man page Source code
rotate3D Man page Source code
rotate90 Man page Source code
scan.dti.tract.file Man page Source code
scan.mrtrix.file Man page Source code
scan.trk.file Man page Source code
scann Man page Source code
skip.connection.bytes Man page Source code
sm0to1 Man page Source code
sm1to0 Man page Source code
split.mrtrix.chunk Man page Source code
stl.format.file.is.ascii Man page Source code
subset.groups Man page Source code
summary.fs.transform Man page Source code
surfaceras.to.ras Man page Source code
surfaceras.to.talairach Man page Source code
talairachras.to.ras Man page Source code
text.line.is.numeric Man page Source code
trackvis.affine.to.rasmm Man page Source code
transform.bbox Man page Source code
transform.descriptor.path Man page Source code
transform.file.sniff.text Man page Source code
transform.flip.handedness Man page Source code
transform.geometry.for.side Man page Source code
transform.matrix.row.lines Man page Source code
transform.value.text Man page Source code
transform.values.text Man page Source code
transform.world.frame Man page Source code
transform2lps Man page Source code
transform2ras Man page Source code
transform2voxel Man page Source code
transform2world Man page Source code
translate.mri.dtype Man page Source code
trk.track.iterator Man page Source code
validate.bbox Man page Source code
validate.dti.gradients Man page Source code
validate.fs.transform Man page Source code
validate_allocation_size Man page Source code
vertex.euclid.dist Man page Source code
vertexdists.to.point Man page Source code
volume.descriptor Man page Source code
volume.geometry Man page Source code
vtk.as.indices Man page Source code
vtk.cell.section.layout Man page Source code
vtk.check.triangles Man page Source code
vtk.data.type.info Man page Source code
vtk.next.line Man page Source code
vtk.next.section Man page Source code
vtk.parse.cell.section Man page Source code
vtk.parse.count Man page Source code
vtk.peek.line Man page Source code
vtk.read.header Man page Source code
vtk.reader.bytes Man page Source code
vtk.reader.close Man page Source code
vtk.reader.fill Man page Source code
vtk.reader.new Man page Source code
vtk.reader.numbers Man page Source code
vtk.reader.peek Man page Source code
vtk.section.values Man page Source code
vtk.section.values.ascii Man page Source code
vtk.split.line Man page Source code
vtk.write.surface.ascii Man page Source code
vtk.write.surface.binary Man page Source code
write.analyze Man page Source code
write.analyze.char.field Man page Source code
write.analyze.header.internal Man page Source code
write.atlas.to.lut.and.csv Man page Source code
write.cifti Man page Source code
write.dti.bval Man page Source code
write.dti.bvec Man page Source code
write.dti.grad Man page Source code
write.dti.tck Man page Source code
write.dti.trk Man page Source code
write.dti.tsf Man page Source code
write.fs.annot Man page Source code
write.fs.annot.gii Man page Source code
write.fs.colortable Man page Source code
write.fs.connectome.cifti Man page Source code
write.fs.curv Man page Source code
write.fs.label Man page Source code
write.fs.label.gii Man page Source code
write.fs.mgh Man page Source code
write.fs.morph Man page Source code
write.fs.morph.asc Man page Source code
write.fs.morph.cifti Man page Source code
write.fs.morph.gii Man page Source code
write.fs.morph.ni1 Man page Source code
write.fs.morph.ni2 Man page Source code
write.fs.morph.smp Man page Source code
write.fs.morph.txt Man page Source code
write.fs.parcellated.cifti Man page Source code
write.fs.parcellation.cifti Man page Source code
write.fs.patch Man page Source code
write.fs.series.cifti Man page Source code
write.fs.surface Man page Source code
write.fs.surface.asc Man page Source code
write.fs.surface.bvsrf Man page Source code
write.fs.surface.byu Man page Source code
write.fs.surface.gii Man page Source code
write.fs.surface.mz3 Man page Source code
write.fs.surface.obj Man page Source code
write.fs.surface.off Man page Source code
write.fs.surface.off.ply2 Man page Source code
write.fs.surface.ply Man page Source code
write.fs.surface.ply2 Man page Source code
write.fs.surface.stl Man page Source code
write.fs.surface.vtk Man page Source code
write.fs.transform Man page Source code
write.fs.transform.dat Man page Source code
write.fs.transform.fslmat Man page Source code
write.fs.transform.itk Man page Source code
write.fs.transform.lta Man page Source code
write.fs.transform.xfm Man page Source code
write.fs.volume Man page Source code
write.fs.weight Man page Source code
write.fs.weight.asc Man page Source code
write.mrtrix.streamlines Man page Source code
write.nifti1 Man page
write.nifti1.data.internal Man page
write.nifti1.header.internal Man page
write.nifti2 Man page Source code
write.smp.brainvoyager Man page Source code
write.smp.brainvoyager.v2 Man page Source code
write.smp.brainvoyager.v3or4or5 Man page Source code
write.stl.ascii Man page Source code
write.stl.binary Man page Source code
write.trk.header Man page Source code
xml_node_gifti_MD Man page Source code
xml_node_gifti_coordtransform Man page Source code
xml_node_gifti_label Man page Source code
xml_node_gifti_label_table Man page Source code
xml_node_gifti_label_table_from_annot Man page Source code
freesurferformats documentation built on Sept. 25, 2026, 1:07 a.m.