mapToColors

Convert intensity values (e.g., a 2D slice) into a color representation for
plotting and overlays.

A collection of data structures and methods for handling volumetric
brain imaging data, with a focus on functional magnetic resonance imaging (fMRI). Provides efficient
representations for three-dimensional and four-dimensional neuroimaging data through sparse and dense array
implementations, memory-mapped file access for large datasets, and
spatial transformation capabilities. Implements methods for image resampling,
spatial filtering, region of interest analysis, and connected component labeling. General introduction
to fMRI analysis can be found in Poldrack et al. (2024, "Handbook of functional MRI data analysis",
<ISBN:9781108795760>).

Bradley Buchsbaum

neuroim2

Data Structures for Brain Imaging Data

mapToColors function

<dl><dt>imslice</dt>
<dd>A numeric vector or array of intensities.</dd>
<dt>col</dt>
<dd>A vector of colors used as a lookup table.</dd>
<dt>zero_col</dt>
<dd>Color used for exactly-zero intensities (defaults to transparent).</dd>
<dt>alpha</dt>
<dd>Global alpha multiplier applied to all colors when <code>alpha &lt; 1</code>.</dd>
<dt>irange</dt>
<dd>Intensity range used to normalize values before mapping to <code>col</code>.</dd>
<dt>threshold</dt>
<dd>Optional length-2 numeric vector. If <code>diff(threshold) &gt; 0</code>,
values within <code>[threshold[1], threshold[2]]</code> are set to transparent.</dd></dl>

Arguments

Map intensity values to colors — mapToColors

<dl>

<dt>imslice</dt>
<dd>A numeric vector or array of intensities.</dd>


<dt>col</dt>
<dd>A vector of colors used as a lookup table.</dd>


<dt>zero_col</dt>
<dd>Color used for exactly-zero intensities (defaults to transparent).</dd>


<dt>alpha</dt>
<dd>Global alpha multiplier applied to all colors when <code>alpha &lt; 1</code>.</dd>


<dt>irange</dt>
<dd>Intensity range used to normalize values before mapping to <code>col</code>.</dd>


<dt>threshold</dt>
<dd>Optional length-2 numeric vector. If <code>diff(threshold) &gt; 0</code>,
values within <code>[threshold[1], threshold[2]]</code> are set to transparent.</dd>

</dl>

mapToColors: Map intensity values to colors

Description

Usage

Value

Arguments