fmrireport

fmrireport generates publication-oriented PDF reports for fitted fmrireg::fmri_lm models. It also provides a standalone cluster_table() function for building COBIDAS-compliant activation tables from any statistical brain volume.

Documentation

Full documentation and vignettes: https://bbuchsbaum.github.io/fmrireport/

Installation

# install.packages("remotes")
remotes::install_github("bbuchsbaum/fmrireport")

Quick example

library(fmrireport)
library(neuroim2)

# Create a synthetic t-stat volume
set.seed(42)
sp <- NeuroSpace(c(64, 64, 40), spacing = c(3, 3, 3))
arr <- array(rnorm(64 * 64 * 40), c(64, 64, 40))
arr[20:28, 25:33, 15:22] <- arr[20:28, 25:33, 15:22] + 5

vol <- NeuroVol(arr, sp)
ct <- cluster_table(vol, threshold = 3.0, stat_type = "t", df = 50)
print(ct)

Full PDF report

library(fmrireg)

# fit <- fmri_lm(...)
# report(fit, output_file = "my_analysis.pdf")

Synthetic demo reports

Rscript inst/examples/fmri_lm_report_demo.R /tmp/fmrireport-report-examples

This writes three complete example reports (matrix, spatial, spatial+atlas).