# Slice visualization with neuroim2

## Quick start: `plot()`

The simplest way to visualize a volume is the S4 `plot()` method. It shows a 3 x 3 montage of evenly-spaced axial slices with a perceptually uniform grayscale palette and clean theme.

    plot(vol)                       # 3x3 montage, grayscale
    plot(vol, cmap = "viridis")     # different palette
    plot(vol, overlay)              # overlay with inferno palette, alpha = 0.5
    plot(vol, overlay, ov_alpha = 0.7, ov_thresh = 2)

For more control — coronal/sagittal planes, downsampling, custom facet layouts — the dedicated helpers below give full flexibility.

## Why these helpers?

Neuroimaging images are large, orientation-sensitive rasters. The goal of these helpers is to make reasonable defaults easy to use: perceptually uniform palettes, robust scaling, fixed aspect ratios, and clean legends — without extra heavy dependencies or any JavaScript.

This vignette shows how to:

- Build publication-ready montages
- Create a compact orthogonal (three-plane) view with crosshairs
- Overlay a statistical map on a structural background (threshold + alpha)

The helpers used here are:

- `resolve_cmap()`, `scale_fill_neuro()`, `theme_neuro()`
- `plot_montage()`, `plot_ortho()`, `plot_overlay()`
- `annotate_orientation()`

## Getting a demo volume

The examples below try to read a sample NIfTI included with the package. If that is not available, they create a small synthetic 3D volume and wrap it in `NeuroVol`. Either way, the rest of the code is identical.

    set.seed(1)

    make_synthetic_vol <- function(dims = c(96, 96, 72), vox = c(2, 2, 2)) {
      i <- array(rep(seq_len(dims[1]), times = dims[2]*dims[3]), dims)
      j <- array(rep(rep(seq_len(dims[2]), each = dims[1]), times = dims[3]), dims)
      k <- array(rep(seq_len(dims[3]), each = dims[1]*dims[2]), dims)

      c0 <- dims / 2
      g1 <- exp(-((i - c0[1])^2 + (j - c0[2])^2 + (k - c0[3])^2) / (2*(min(dims)/4)^2))
      g2 <- 0.5 * exp(-((i - (c0[1] + 15))^2 + (j - (c0[2] - 10))^2 + (k - (c0[3] + 8))^2) / (2*(min(dims)/6)^2))
      x  <- g1 + g2 + 0.05 * array(stats::rnorm(prod(dims)), dims)

      sp <- NeuroSpace(dims, spacing = vox)
      NeuroVol(x, sp)
    }

    # Prefer an included demo file. Use a real example from inst/extdata.
    demo_path <- system.file("extdata", "mni_downsampled.nii.gz", package = "neuroim2")

    t1 <- if (nzchar(demo_path)) {
      read_vol(demo_path)
    } else {
      make_synthetic_vol()
    }

    dims <- dim(t1)

    # Build a synthetic "z-statistic" overlay matched to t1's dims
    mk_blob <- function(mu, sigma = 8) {
      i <- array(rep(seq_len(dims[1]), times = dims[2]*dims[3]), dims)
      j <- array(rep(rep(seq_len(dims[2]), each = dims[1]), times = dims[3]), dims)
      k <- array(rep(seq_len(dims[3]), each = dims[1]*dims[2]), dims)
      exp(-((i - mu[1])^2 + (j - mu[2])^2 + (k - mu[3])^2) / (2*sigma^2))
    }
    ov_arr <- 3.5 * mk_blob(mu = round(dims * c(.60, .45, .55)), sigma = 7) -
              3.2 * mk_blob(mu = round(dims * c(.35, .72, .40)), sigma = 6) +
              0.3 * array(stats::rnorm(prod(dims)), dims)

    overlay <- NeuroVol(ov_arr, space(t1))

## 1) Montages that read well at a glance

The montage helper facets a single ggplot object—so you get a shared colorbar, clean panel labels, and proper aspect ratio.

    # Choose a sensible set of axial slices
    zlevels <- unique(round(seq( round(dims[3]*.25), round(dims[3]*.85), length.out = 12 )))

    p <- plot_montage(
      t1, zlevels = zlevels, along = 3,
      cmap = "grays", range = "robust", probs = c(.02, .98),
      ncol = 6, title = "Axial montage (robust scaling)"
    )
    p + theme_neuro()

Notes

- `range = "robust"` uses quantiles (default 2–98%) to ignore outliers.
- `coord_fixed()` + reversed y are handled internally to preserve geometry and radiological convention.
- Use `downsample = 2` (or higher) when plotting huge volumes interactively.

    plot_montage(
      t1, zlevels = zlevels, along = 3,
      cmap = "grays", range = "robust", ncol = 6, downsample = 2,
      title = "Downsampled montage (for speed)"
    )

## 2) Orthogonal three‑plane view (with crosshairs)

`plot_ortho()` produces aligned sagittal, coronal, and axial slices with a shared scale, optional crosshairs, and compact orientation glyphs.

    center_voxel <- round(dim(t1) / 2)
    plot_ortho(
      t1, coord = center_voxel, unit = "index",
      cmap = "grays", range = "robust",
      crosshair = TRUE, annotate = TRUE
    )

Tip: If you have MNI/world coordinates, pass `unit = "mm"` and a length‑3 numeric; internally it will convert using `coord_to_grid(space(vol), …)` if available.

## 3) Overlaying an activation map on a structural background

The overlay compositor colorizes each layer independently (so each can use its own limits and palette) and stacks them as rasters. No extra packages required.

    plot_overlay(
      bgvol = t1, overlay = overlay,
      zlevels = zlevels[seq(2, length(zlevels), by = 2)],  # fewer panels for the vignette
      bg_cmap = "grays", ov_cmap = "inferno",
      bg_range = "robust", ov_range = "robust", probs = c(.02, .98),
      ov_thresh = 2.5,   # make weaker signal transparent
      ov_alpha  = 0.65,
      ncol = 3, title = "Statistical overlay (threshold 2.5, alpha 0.65)"
    )

## 4) Palettes and aesthetics

All examples above use neuro‑friendly defaults:

- Palettes: `resolve_cmap()` wraps base R’s `hcl.colors()` with aliases like “grays”, “viridis”, “inferno”—and safe fallbacks.
- Theme: `theme_neuro()` keeps panels quiet and legends slim.
- Legend: one shared colorbar for facetted montages via `scale_fill_neuro()`.

You can switch palettes easily:

    plot_montage(
      t1, zlevels = zlevels[1:6], along = 3,
      cmap = "viridis", range = "robust", ncol = 6,
      title = "Same data, Viridis palette"
    )

## 5) Practical tips

- Choose slices with meaning. Use mm positions (if you have an affine) or meaningful indices; label strips are handled for you by the helper.
- Speed vs. fidelity. Use `downsample` for exploration; keep `downsample = 1` for final figures.
- Consistent limits. For side‑by‑side comparisons, compute limits on a combined set of values (the helpers do this for orthogonal panels automatically).

## Reproducibility

    sessionInfo()
    ## R version 4.5.1 (2025-06-13)
    ## Platform: aarch64-apple-darwin20
    ## Running under: macOS Sonoma 14.3
    ##
    ## Matrix products: default
    ## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
    ## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
    ##
    ## locale:
    ## [1] C/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
    ##
    ## time zone: America/Toronto
    ## tzcode source: internal
    ##
    ## attached base packages:
    ## [1] stats     graphics  grDevices utils     datasets  methods   base
    ##
    ## other attached packages:
    ## [1] ggplot2_4.0.2   purrr_1.2.1     neuroim2_0.13.0 Matrix_1.7-3
    ##
    ## loaded via a namespace (and not attached):
    ##  [1] sass_0.4.10           generics_0.1.4        mmap_0.6-24
    ##  [4] stringi_1.8.7         lattice_0.22-7        digest_0.6.39
    ##  [7] magrittr_2.0.5        bigstatsr_1.6.2       evaluate_1.0.5
    ## [10] grid_4.5.1            RColorBrewer_1.1-3    iterators_1.0.14
    ## [13] rmio_0.4.0            fastmap_1.2.0         foreach_1.5.2
    ## [16] doParallel_1.0.17     jsonlite_2.0.0        RNifti_1.9.0
    ## [19] deflist_0.2.0         scales_1.4.0          albersdown_1.0.0
    ## [22] codetools_0.2-20      jquerylib_0.1.4       cli_3.6.5
    ## [25] rlang_1.1.7           cowplot_1.2.0         splines_4.5.1
    ## [28] withr_3.0.2           cachem_1.1.0          yaml_2.3.12
    ## [31] otel_0.2.0            flock_0.7             tools_4.5.1
    ## [34] parallel_4.5.1        memoise_2.0.1         bigassertr_0.1.7
    ## [37] dplyr_1.2.1           assertthat_0.2.1      vctrs_0.7.2
    ## [40] R6_2.6.1              lifecycle_1.0.5       bigparallelr_0.3.2
    ## [43] stringr_1.6.0         dbscan_1.2.4          pkgconfig_2.0.3
    ## [46] RcppParallel_5.1.11-2 pillar_1.11.1         bslib_0.10.0
    ## [49] gtable_0.3.6          glue_1.8.0            Rcpp_1.1.1
    ## [52] xfun_0.57             tibble_3.3.1          tidyselect_1.2.1
    ## [55] knitr_1.51            farver_2.1.2          htmltools_0.5.9
    ## [58] labeling_0.4.3        RNiftyReg_2.8.5       rmarkdown_2.31
    ## [61] compiler_4.5.1        S7_0.2.1