plot_ortho

Creates axial, coronal, and sagittal panels at a given coordinate with
harmonized aesthetics. Returns (invisibly) the three ggplot objects after
printing them in a single row using base grid (no extra deps).

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

plot_ortho function

<dl><dt>vol</dt>
<dd>A 3D volume handled by `slice()`.</dd>
<dt>coord</dt>
<dd>Length-3 coordinate of the target point. Interpreted as voxel
indices by default; set `unit = "mm"` to convert using `coord_to_grid()`
if available in your environment.</dd>
<dt>unit</dt>
<dd>"index" or "mm".</dd>
<dt>cmap</dt>
<dd>Palette for the slices.</dd>
<dt>range</dt>
<dd>"robust" or "data" for intensity limits shared by all panels.</dd>
<dt>probs</dt>
<dd>Quantiles for robust range.</dd>
<dt>crosshair</dt>
<dd>Logical; draw crosshair lines.</dd>
<dt>annotate</dt>
<dd>Logical; add orientation glyphs.</dd>
<dt>downsample</dt>
<dd>Integer decimation for speed.</dd></dl>

Arguments

Orthogonal three-plane view with optional crosshairs — plot_ortho

<dl>

<dt>vol</dt>
<dd>A 3D volume handled by `slice()`.</dd>


<dt>coord</dt>
<dd>Length-3 coordinate of the target point. Interpreted as voxel
indices by default; set `unit = "mm"` to convert using `coord_to_grid()`
if available in your environment.</dd>


<dt>unit</dt>
<dd>"index" or "mm".</dd>


<dt>cmap</dt>
<dd>Palette for the slices.</dd>


<dt>range</dt>
<dd>"robust" or "data" for intensity limits shared by all panels.</dd>


<dt>probs</dt>
<dd>Quantiles for robust range.</dd>


<dt>crosshair</dt>
<dd>Logical; draw crosshair lines.</dd>


<dt>annotate</dt>
<dd>Logical; add orientation glyphs.</dd>


<dt>downsample</dt>
<dd>Integer decimation for speed.</dd>

</dl>

plot_ortho: Orthogonal three-plane view with optional crosshairs

Description

Usage

Arguments