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freesurferformats

Star Watch Copy Code

Read and Write 'FreeSurfer' Neuroimaging File Formats

View on CRAN: Click here

Download and install freesurferformats package within the R console
Install from CRAN:

 install.packages("freesurferformats")

Install from Github:

 library("remotes")

                        install_github("cran/freesurferformats")

Install by package version:

 library("remotes")

                        install_version("freesurferformats", "0.1.18")

Attach the package and use:

 library("freesurferformats")

Maintained by
Tim Schäfer
[Scholar Profile | Author Map]

All associated links for this package

First Published: 2019-09-04

Latest Update: 2024-02-02

Description:

Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' formats. This includes, but is not limited to, the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.

How to cite:

Tim Schäfer (2019). freesurferformats: Read and Write 'FreeSurfer' Neuroimaging File Formats. R package version 0.1.18, https://cran.r-project.org/web/packages/freesurferformats. Accessed 29 Jan. 2025.

Previous versions and publish date:

0.1.0 (2019-09-04 10:20), 0.1.1 (2019-09-13 15:00), 0.1.2 (2019-10-02 21:10), 0.1.3 (2019-10-15 23:10), 0.1.4 (2019-11-06 19:00), 0.1.5 (2019-11-12 19:40), 0.1.6 (2019-11-27 14:50), 0.1.7 (2020-01-07 15:10), 0.1.8 (2020-02-17 17:40), 0.1.9 (2020-04-14 20:10), 0.1.10 (2020-05-13 20:50), 0.1.11 (2020-06-17 14:50), 0.1.12 (2020-08-26 18:11), 0.1.13 (2020-09-21 23:40), 0.1.14 (2021-01-17 14:20), 0.1.15 (2021-05-25 17:00), 0.1.16 (2021-11-07 17:40), 0.1.17 (2022-02-11 15:30)

Other packages that cited freesurferformats R package

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Other R packages that freesurferformats depends, imports, suggests or enhances

View freesurferformats dependency map

Complete documentation for freesurferformats

View documentation PDF

Functions, R codes and Examples using the freesurferformats R package

Some associated functions: adjust.face.indices.to . annot.max.region.idx . annot.unique . assert.surface . bvsmp . cdata . check.dtype.for.data . check_data_and_settings_consistency . closest.vert.to.point . colortable.from.annot . coord.to.key . delete_all_opt_data . doapply.transform.mtx . download_opt_data . euclidian.dist . faces.quad.to.tris . faces.tris.to.quad . fileopen.gz.or.not . filepath.ends.with . fixed.vec.format.int . flip2D . flip3D . fread3 . fs.get.morph.file.ext.for.format . fs.get.morph.file.format.from.filename . fs.patch . fs.surface.to.tmesh3d . fwrite3 . get.dti.trk.endianness . get.slice.orientation . get_opt_data_filepath . gifti_writer . gifti_xml . gifti_xml_add_global_metadata . gifti_xml_write . giftixml_add_labeltable_from_annot . giftixml_add_labeltable_posneg . guess.filename.is.gzipped . has_pandoc . int.to.col.brainvoyager . is.bvsmp . is.fs.annot . is.fs.label . is.fs.surface . is.fs.volume . is.mghheader . linesplit.fixed . list_opt_data . mgh.is.conformed . mghheader.centervoxelRAS.from.firstvoxelRAS . mghheader.crs.orientation . mghheader.is.conformed . mghheader.is.ras.valid . mghheader . mghheader.primary.slice.direction . mghheader.ras2vox . mghheader.ras2vox.tkreg . mghheader.scanner2tkreg . mghheader.tkreg2scanner . mghheader.update.from.vox2ras . mghheader.vox2ras . mghheader.vox2ras.tkreg . mghheader.vox2vox . mni152reg . mri_dtype_numbytes . ni1header.for.data . ni1header.template . ni2header.for.data . ni2header.template . nifti.datadim.from.dimfield . nifti.datadim.to.dimfield . nifti.dtype.info . nifti.field.check.length . nifti.field.check.nchar.max . nifti.file.uses.fshack . nifti.file.version . nifti.header.check . nifti.space.info . nifti.time.info . nifti.transform.type.name . parse.stl.ascii.face . parse.transform.matrix.lines . ply.header.lines . polygon.soup.to.indexed.mesh . print.fs.annot . print.fs.label . print.fs.patch . print.fs.surface . print.fs.volume . ras.to.surfaceras . ras.to.talairachras . read.dti.tck . read.dti.trk . read.dti.tsf . read.element.counts.ply.header . read.fixed.char.binary . read.fs.annot.gii . read.fs.annot . read.fs.colortable . read.fs.curv . read.fs.gca . read.fs.label.gii . read.fs.label.native . read.fs.label . read.fs.mgh . read.fs.morph.asc . read.fs.morph.bvsmp . read.fs.morph.cifti . read.fs.morph.gii . read.fs.morph.ni1 . read.fs.morph.ni2 . read.fs.morph.nii . read.fs.morph . read.fs.morph.txt . read.fs.patch.asc . read.fs.patch . read.fs.surface.asc . read.fs.surface.bvsrf . read.fs.surface.byu . read.fs.surface.geo . read.fs.surface.gii . read.fs.surface.ico . read.fs.surface.mz3 . read.fs.surface . read.fs.surfacej . read.fs.surface.off . read.fs.surface.ply . read.fs.surface.stl.ascii . read.fs.surface.stl.bin . read.fs.surface.stl . read.fs.surface.vtk . read.fs.transform.dat . read.fs.transform.lta . read.fs.transform . read.fs.transform.xfm . read.fs.volume.nii . read.fs.volume . read.fs.weight.asc . read.fs.weight . read.mesh.brainvoyager . read.nifti1.data . read.nifti1.header.internal . read.nifti1.header . read.nifti2.data . read.nifti2.header.internal . read.nifti2.header . read.smp.brainvoyager . read.smp.brainvoyager.v1or2 . read.smp.brainvoyager.v3 . read.smp.brainvoyager.v4or5 . read_nisurface . read_nisurfacefile.fsascii . read_nisurfacefile.fsnative . read_nisurfacefile.gifti . read_nisurfacefile . readable.files . readcolortable . readcolortable_oldformat . rotate2D . rotate3D . rotate90 . scann . sm0to1 . sm1to0 . stl.format.file.is.ascii . surfaceras.to.ras . surfaceras.to.talairach . talairachras.to.ras . translate.mri.dtype . vertex.euclid.dist . vertexdists.to.point . write.fs.annot.gii . write.fs.annot . write.fs.colortable . write.fs.curv . write.fs.label.gii . write.fs.label . write.fs.mgh . write.fs.morph.asc . write.fs.morph.gii . write.fs.morph.ni1 . write.fs.morph.ni2 . write.fs.morph . write.fs.morph.smp . write.fs.morph.txt . write.fs.patch . write.fs.surface.asc . write.fs.surface.bvsrf . write.fs.surface.byu . write.fs.surface.gii . write.fs.surface.mz3 . write.fs.surface . write.fs.surfacej . write.fs.surface.off . write.fs.surface.off.ply2 . write.fs.surface.ply . write.fs.surface.ply2 . write.fs.surface.vtk . write.fs.weight.asc . write.fs.weight . write.nifti1 . write.nifti2 . write.smp.brainvoyager . write.smp.brainvoyager.v2 . write.smp.brainvoyager.v3or4or5 . xml_node_gifti_MD . xml_node_gifti_coordtransform . xml_node_gifti_label . xml_node_gifti_label_table . xml_node_gifti_label_table_from_annot .
Some associated R codes: brainvoyager.R . cifti.R . gifti_writer.R . gifti_xml_tools.R . helpers.R . mghheader.R . nifti_common.R . nifti_to_mgh.R . optdata.R . read_dti_tck.R . read_dti_trk.R . read_fs_annot.R . read_fs_curv.R . read_fs_label.R . read_fs_mgh.R . read_fs_patch.R . read_fs_surface.R . read_fs_transform.R . read_fs_volume.R . read_fs_weight.R . read_nifti1.R . read_nifti2.R . read_nisurface.R . rotate3d.R . surface_dist.R . write_fs_annot.R . write_fs_curv.R . write_fs_label.R . write_fs_mgh.R . write_fs_patch.R . write_fs_surface.R . write_fs_weight.R . write_nifti1.R . write_nifti2.R . Full freesurferformats package functions and examples

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