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bvsmp()
|
Create new bvsmp instance encoding morph data for Brainvoyager. |
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cdata()
|
Create CDATA element string from string. |
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colortable.from.annot()
|
Extract color lookup table (LUT) from annotation. |
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delete_all_opt_data()
|
Delete all data in the package cache. |
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download_opt_data()
|
Download optional data for the freesurferformats package. |
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faces.quad.to.tris()
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Convert quadrangular faces or polygons to triangular ones. |
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faces.tris.to.quad()
|
Convert tris faces to quad faces by simple merging. |
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flip2D()
|
Flip a 2D matrix. |
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flip3D()
|
Flip a 3D array along an axis. |
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fs.get.morph.file.ext.for.format()
|
Determine morphometry file extension from format |
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fs.get.morph.file.format.from.filename()
|
Determine morphometry file format from filename |
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fs.patch()
|
Constructor for fs.patch |
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get_opt_data_filepath()
|
Access a single file from the package cache by its file name. |
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gifti_writer()
|
Write data to a gifti file. |
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gifti_xml()
|
Get GIFTI XML representation of data. |
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gifti_xml_add_global_metadata()
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Add metadata to GIFTI XML tree. |
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gifti_xml_write()
|
Write XML tree to a gifti file. |
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giftixml_add_labeltable_from_annot()
|
Add a label tabel from an annotation to a GIFTI XML tree. |
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is.bvsmp()
|
Check whether object is a bvsmp instance. |
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is.fs.annot()
|
Check whether object is an fs.annot |
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is.fs.label()
|
Check whether object is an fs.label |
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is.fs.surface()
|
Check whether object is an fs.surface |
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is.fs.volume()
|
Check whether object is an fs.volume |
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is.mghheader()
|
Check whether object is an mghheader |
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list_opt_data()
|
Get file names available in package cache. |
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mghheader.centervoxelRAS.from.firstvoxelRAS()
|
Compute RAS coords of center voxel. |
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mghheader.crs.orientation()
|
Compute MGH volume orientation string. |
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mghheader.is.conformed()
|
Determine whether an MGH volume is conformed. |
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mghheader.is.ras.valid()
|
Check whether header contains valid ras information |
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mghheader.primary.slice.direction()
|
Compute MGH primary slice direction |
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mghheader.ras2vox()
|
Compute ras2vox matrix from basic MGH header fields. |
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mghheader.ras2vox.tkreg()
|
Compute ras2vox-tkreg matrix from basic MGH header fields. |
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mghheader.scanner2tkreg()
|
Compute scanner-RAS 2 tkreg-RAS matrix from basic MGH header fields. |
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mghheader.tkreg2scanner()
|
Compute tkreg-RAS to scanner-RAS matrix from basic MGH header fields. |
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mghheader.update.from.vox2ras()
|
Update mghheader fields from vox2ras matrix. |
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mghheader.vox2ras()
|
Compute vox2ras matrix from basic MGH header fields. |
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mghheader.vox2ras.tkreg()
|
Compute vox2ras-tkreg matrix from basic MGH header fields. |
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mghheader.vox2vox()
|
Compute vox2vox matrix between two volumes. |
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ni1header.for.data()
|
Create NIFTI v1 header suitable for given data. |
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ni1header.template()
|
Create a template NIFTI v1 header. You will have to adapt it for your use case. |
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ni2header.for.data()
|
Create NIFTI v2 header suitable for given data. |
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ni2header.template()
|
Create a template NIFTI v2 header. You will have to adapt it for your use case. |
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nifti.datadim.from.dimfield()
|
Compute data dimensions from the 'dim' field of the NIFTI (v1 or v2) header. |
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nifti.datadim.to.dimfield()
|
Compute NIFTI dim field for data dimension. |
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nifti.file.uses.fshack()
|
Determine whether a NIFTI file uses the FreeSurfer hack. |
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nifti.file.version()
|
Determine NIFTI file version information and whether file is a NIFTI file. |
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nifti.header.check()
|
Perform basic sanity checks on NIFTI header data. These are in no way meant to be exhaustive. |
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print(<fs.annot>)
|
Print description of a brain atlas or annotation. |
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print(<fs.label>)
|
Print description of a brain surface label. |
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print(<fs.patch>)
|
Print description of a brain surface patch. |
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print(<fs.surface>)
|
Print description of a brain surface. |
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print(<fs.volume>)
|
Print description of a brain volume. |
|
ras.to.surfaceras()
|
Translate RAS coordinates, as used in volumes by applying vox2ras, to surface RAS. |
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ras.to.talairachras()
|
Compute MNI talairach coordinates from RAS coords. |
|
read.fs.annot()
|
Read file in FreeSurfer annotation format |
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read.fs.annot.gii()
|
Read an annotation or label in GIFTI format. |
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read.fs.colortable()
|
Read colortable file in FreeSurfer ASCII LUT format. |
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read.fs.curv()
|
Read file in FreeSurfer curv format |
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read.fs.gca()
|
Read FreeSurfer GCA file. |
|
read.fs.label()
|
Read a label file. |
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read.fs.label.gii()
|
Read a label from a GIFTI label/annotation file. |
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read.fs.label.native()
|
Read file in FreeSurfer label format |
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read.fs.mgh()
|
Read file in FreeSurfer MGH or MGZ format |
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read.fs.morph()
|
Read morphometry data file in any FreeSurfer format. |
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read.fs.morph.asc()
|
Read morphometry data from ASCII curv format file |
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read.fs.morph.bvsmp()
|
Read Brainvoyager vertex-wise statistical surface data from SMP file. |
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read.fs.morph.cifti()
|
Read surface morphometry data from CIFTI dscalar files. |
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read.fs.morph.gii()
|
Read morphometry data file in GIFTI format. |
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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. |
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read.fs.morph.nii()
|
Read morphometry data from FreeSurfer NIFTI format files, determine NIFTI version automatically. |
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read.fs.morph.txt()
|
Read morphometry data from plain text file |
|
read.fs.patch()
|
Read FreeSurfer binary or ASCII patch file. |
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read.fs.patch.asc()
|
Read FreeSurfer ASCII format patch. |
|
read.fs.surface()
|
Read file in FreeSurfer surface format or various mesh formats. |
|
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. |
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read.fs.surface.obj()
|
Read OBJ format mesh as surface. |
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read.fs.surface.off()
|
Read Object File Format (OFF) mesh as surface. |
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read.fs.surface.ply()
|
Read Stanford PLY format mesh as surface. |
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read.fs.surface.stl()
|
Read mesh in STL format, auto-detecting ASCII versus binary format version. |
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read.fs.surface.stl.bin()
|
Read surface mesh in STL binary format. |
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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 array (LTA) file. |
|
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` instance with complete header. |
|
read.fs.weight()
|
Read file in FreeSurfer weight or w format |
|
read.mesh.brainvoyager()
|
Read Brainvoyager srf format (.srf) mesh. |
|
read.nifti1.data()
|
Read raw NIFTI v1 data from file (which may contain the FreeSurfer hack). |
|
read.nifti1.header()
|
Read NIFTI v1 header from file (which may contain the FreeSurfer hack). |
|
read.nifti2.data()
|
Read raw data from NIFTI v2 file. |
|
read.nifti2.header()
|
Read NIFTI v2 header from file. |
|
read.smp.brainvoyager()
|
Read Brainvoyager statistical surface results from SMP 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. |
|
readable.files()
|
Find files with the given base name and extensions that exist. |
|
rotate2D()
|
Rotate a 2D matrix in 90 degree steps. |
|
rotate3D()
|
Rotate a 3D array in 90 degree steps. |
|
sm0to1()
|
Adapt spatial transformation matrix for 1-based indices. |
|
sm1to0()
|
Adapt spatial transformation matrix for 0-based indices. |
|
surfaceras.to.ras()
|
Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS. |
|
surfaceras.to.talairach()
|
Compute Talairach RAS for surface RAS (e.g., vertex coordinates). |
|
talairachras.to.ras()
|
Compute MNI talairach coordinates from RAS coords. |
|
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 file name. |
|
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.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. |
|
xml_node_gifti_coordtransform()
|
Create XML GIFTI CoordinateSystemTransformMatrix node. |