write.fs.colortable

Write the colortable to a text file in FreeSurfer ASCII colortable lookup table (LUT) format. An example file is `FREESURFER_HOME/FreeSurferColorLUT.txt`.

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

write.fs.colortable function

<dl><dt>filepath, </dt>
<dd>string. Full path to the output colormap file.</dd>
<dt>colortable</dt>
<dd>data.frame, a colortable as read by <code>read.fs.colortable</code>. Must contain the following columns: 'struct_name': character string, the label name. 'r': integer in range 0-255, the RGBA color value for the red channel. 'g': same for green channel. 'b': same for blue channel. 'a': same for alpha (transparency) channel. Can contain the following column: 'struct_index': integer, index of the struct entry. If this column does not exist, sequential indices starting at zero are created.</dd></dl>

Arguments

Write colortable file in FreeSurfer ASCII LUT format. — write.fs.colortable

<dl>

<dt>filepath, </dt>
<dd>string. Full path to the output colormap file.</dd>


<dt>colortable</dt>
<dd>data.frame, a colortable as read by <code>read.fs.colortable</code>. Must contain the following columns: 'struct_name': character string, the label name. 'r': integer in range 0-255, the RGBA color value for the red channel. 'g': same for green channel. 'b': same for blue channel. 'a': same for alpha (transparency) channel. Can contain the following column: 'struct_index': integer, index of the struct entry. If this column does not exist, sequential indices starting at zero are created.</dd>

</dl>

write.fs.colortable: Write colortable file in FreeSurfer ASCII LUT format.

Description

Usage

Value

Arguments

See Also