Package 'fmrireport'

Coerce cluster_table to a Flat data.frame

Description

Produces a flat data.frame suitable for table rendering. Cluster rows have all columns populated; sub-peak rows have k and volume_mm3 set to NA.

Usage

## S3 method for class 'cluster_table'
as.data.frame(
  x,
  row.names = NULL,
  optional = FALSE,
  max_clusters = 30L,
  max_sub_peaks = 3L,
  ...
)

Arguments

x	A cluster_table object.
row.names	Ignored.
optional	Ignored.
max_clusters	Maximum clusters to include.
max_sub_peaks	Maximum sub-peaks per cluster.
...	Ignored.

Value

A data.frame.

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Build a Publication-Quality Activation Cluster Table

Description

Detects suprathreshold clusters in a statistical brain volume and returns a structured table of cluster-level and peak-level statistics suitable for publication (NeuroImage / HBM / COBIDAS compliant).

Usage

cluster_table(
  vol,
  threshold,
  atlas = NULL,
  stat_type = c("t", "z", "F", "other"),
  df = NULL,
  coord_space = NULL,
  min_cluster_size = 10L,
  local_maxima_dist = 15,
  max_peaks = 3L,
  connectivity = c("26-connect", "18-connect", "6-connect"),
  sort_by = c("size", "peak_stat")
)

Arguments

vol	A NeuroVol object containing the statistical map.
threshold	Numeric threshold for cluster detection (absolute value).
atlas	Optional atlas object (e.g., a volatlas from neuroatlas) for anatomical labeling.
stat_type	Type of statistic in the volume: "t", "z", "F", or "other".
df	Degrees of freedom for p-value computation. A single value for t/z statistics, or a length-2 vector c(df1, df2) for F statistics. NULL omits p-values.
coord_space	Character string naming the coordinate space (e.g., "MNI152", "MNI305"). If NULL, inferred from atlas or set to "Unknown".
min_cluster_size	Minimum number of voxels for a cluster to be retained.
local_maxima_dist	Minimum distance (mm) between local maxima within a cluster.
max_peaks	Maximum number of sub-peaks reported per cluster.
connectivity	Voxel connectivity for cluster detection.
sort_by	Sort clusters by "size" (descending) or "peak_stat" (descending absolute value).

Value

An S3 object of class "cluster_table" with elements:

clusters

A data.frame with one row per cluster.

peaks

A data.frame with sub-peaks (local maxima) per cluster.

threshold

The threshold used.

stat_type

The statistic type.

df

Degrees of freedom.

n_clusters

Number of clusters.

coord_space

Coordinate space label.

atlas_name

Name of atlas used, or NA.

---

Format a cluster_table as a tinytable

Description

Returns a tinytable::tt() object with appropriate caption and formatting for Quarto/Typst rendering.

Usage

format_cluster_tt(x, max_clusters = 30L, max_sub_peaks = 3L, digits = 3L, ...)

Arguments

x	A cluster_table object.
max_clusters	Maximum clusters to include.
max_sub_peaks	Maximum sub-peaks per cluster.
digits	Number of digits for rounding numeric columns.
...	Passed to tinytable::tt().

Value

A tinytable object.

---

Print a cluster_table Object

Description

CLI-formatted hierarchical output showing clusters with sub-peaks indented.

Usage

## S3 method for class 'cluster_table'
print(x, max_clusters = 20L, max_sub_peaks = 3L, ...)

Arguments

x	A cluster_table object.
max_clusters	Maximum number of clusters to display.
max_sub_peaks	Maximum sub-peaks per cluster to display.
...	Ignored.

Value

Invisibly returns x.

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Render Analysis Reports

Description

Generic report interface and fmri_lm implementation that renders a publication-style PDF report through Quarto.

Usage

report(x, ...)

## Default S3 method:
report(x, ...)

## S3 method for class 'fmri_lm'
report(
  x,
  output_file = "fmri_lm_report.pdf",
  title = "fMRI GLM Analysis Report",
  author = NULL,
  sections = c("model", "design", "hrf", "estimates", "contrasts", "diagnostics"),
  brain_map_stat = c("tstat", "estimate", "prob"),
  slice_axis = 3L,
  n_slices = 9L,
  threshold = NULL,
  bg_vol = NULL,
  atlas = NULL,
  cluster_thresh = 3,
  min_cluster_size = 10L,
  max_peaks = 15L,
  local_maxima_dist = 15,
  max_sub_peaks = 3L,
  open = interactive(),
  quiet = TRUE,
  ...
)

Arguments

x	Object to report on.
...	Additional arguments passed to methods.
output_file	Output PDF path.
title	Report title.
author	Optional author string.
sections	Sections to include.
brain_map_stat	Statistic for contrast maps: "tstat", "estimate", or "prob".
slice_axis	Axis for montage slicing (1, 2, or 3).
n_slices	Number of slices to render in contrast maps.
threshold	Optional hard threshold for contrast map rendering.
bg_vol	Optional background NeuroVol for overlay plots.
atlas	Optional atlas object for peak labeling.
cluster_thresh	Absolute statistic threshold for peak clustering.
min_cluster_size	Minimum cluster size (voxels) in peak table.
max_peaks	Maximum peaks per contrast table.
local_maxima_dist	Minimum distance (mm) between local maxima within a cluster for sub-peak detection. Default 15.
max_sub_peaks	Maximum number of sub-peaks per cluster in the activation table. Default 3.
open	If TRUE, open the generated PDF after rendering.
quiet	If TRUE, suppress Quarto render logs.

Value

Method-specific report output. For fmri_lm fits, returns the output PDF path invisibly.

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