volume.geometry

Transformation matrices of the voxel-to-voxel kind can only be interpreted relative to the
volumes they relate, so the conversion functions need the geometry of those volumes: their dimensions, voxel
sizes and the matrix that maps voxel indices to RAS coordinates.
The voxel indices are zero-based and the origin of the RAS space is the one used by FreeSurfer for MGH
headers and by NIfTI for the <code>sform</code>, i.e. this is the same convention as <code>mghheader.vox2ras</code>.

internal

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/NIFTI 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.

Tim Schc3<a4>fer

freesurferformats

Read and Write 'FreeSurfer' Neuroimaging File Formats

Tim Schäfer

Van Essen Lab 

Montreal Neurological Institute (MNI) 

volume.geometry function

<dl><dt>volume</dt>
<dd>an <code>fs.volume</code> instance (as returned by <code>read.fs.volume</code> or
<code>read.fs.mgh</code>), a <code>nifti</code> instance (from the <code>oro.nifti</code> package), or a named list with the
entries 'vox2ras_matrix', 'voldim' and 'voxelsize'.</dd></dl>

Arguments

Get the geometry of a volume. — volume.geometry

<dl>

<dt>volume</dt>
<dd>an <code>fs.volume</code> instance (as returned by <code>read.fs.volume</code> or
<code>read.fs.mgh</code>), a <code>nifti</code> instance (from the <code>oro.nifti</code> package), or a named list with the
entries 'vox2ras_matrix', 'voldim' and 'voxelsize'.</dd>

</dl>

volume.geometry: Get the geometry of a volume.

Description

Usage

Value

Arguments