generate_mask_diagnostics: Generate a set of diagnostic images and plots for brain masks...

In UNCDEPENdLab/fmri.pipeline: Analysis of fMRI Data on HPC clusters

Generate a set of diagnostic images and plots for brain masks relative to one another and a template

Description

Generate a set of diagnostic images and plots for brain masks relative to one another and a template

Usage

generate_mask_diagnostics(
  input = NULL,
  reference_mask = NULL,
  reference_t1 = NULL,
  output_directory = NULL,
  generate_automask = NULL,
  generate_run_plots = TRUE,
  ncores = 8L
)

Arguments

input	Can be a character vector of mask files, a gpa object, or a data.frame containing a brain_mask field, or at least a $run_nifti field. If a gpa object is provided, we will use the $run_data data.frame.
reference_mask	a string pointing to the reference mask used for run brain mask comparisons. Must be in the same stereotaxic space and have the same dimensions as the run brain masks.
reference_t1	a string pointing to the T1w image of the reference brain. Used to aid interpretability of brain mask visualizations.
output_directory	a string pointing to a directory for mask diagnostics. Defaults to "mask_diagnostics" in the current directory. This directory will be created if it does not exist.
generate_automask	a logical indicating whether to use AFNI 3dAutomask to generate brain masks if they are not provided in the $brain_mask field. If NULL (default), the user will be prompted for whether they wish to generate missing brain masks. If FALSE, masks will not be generate, and if TRUE, they will be generated.

UNCDEPENdLab/fmri.pipeline documentation built on April 3, 2025, 3:21 p.m.