surfaceras.to.ras

Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS.

Provides functions to read and write neuroimaging data in various file formats, with a focus on 'FreeSurfer' <http://freesurfer.net/> 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.

Tim Schc3<a4>fer

freesurferformats

Read and Write 'FreeSurfer' Neuroimaging File Formats

Tim Schäfer

surfaceras.to.ras function

<dl><dt>header_cras</dt>
<dd>an MGH header instance from which to extract the cras (center RAS), or the cras vector, i.e., a numerical vector of length 3</dd>
<dt>sras_coords</dt>
<dd>nx3 numerical vector, the input surface RAS coordinates. Could be the vertex coordinates of an 'fs.surface' instance, or the RAS coords from a surface label. Use the orig surfaces.</dd>
<dt>first_voxel_RAS</dt>
<dd>the RAS of the first voxel, see <code>mghheader.centervoxelRAS.from.firstvoxelRAS</code> for details. Ignored if 'header_cras' is a vector.</dd>
<dt>invert_transform</dt>
<dd>logical, whether to invert the transform. Do not use this, call <code>link{ras.to.surfaceras}</code> instead.</dd></dl>

Arguments

Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS. — surfaceras.to.ras

<dl>

<dt>header_cras</dt>
<dd>an MGH header instance from which to extract the cras (center RAS), or the cras vector, i.e., a numerical vector of length 3</dd>


<dt>sras_coords</dt>
<dd>nx3 numerical vector, the input surface RAS coordinates. Could be the vertex coordinates of an 'fs.surface' instance, or the RAS coords from a surface label. Use the orig surfaces.</dd>


<dt>first_voxel_RAS</dt>
<dd>the RAS of the first voxel, see <code>mghheader.centervoxelRAS.from.firstvoxelRAS</code> for details. Ignored if 'header_cras' is a vector.</dd>


<dt>invert_transform</dt>
<dd>logical, whether to invert the transform. Do not use this, call <code>link{ras.to.surfaceras}</code> instead.</dd>

</dl>

surfaceras.to.ras: Translate surface RAS coordinates, as used in surface vertices and surface labels, to volume RAS.

Description

Usage

Value

Arguments