setup_l3_models: This function generates the inputs for level 3 analyses,...

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

This function generates the inputs for level 3 analyses, where multi-subject data are analyzed in group analyses.

Description

This function generates the inputs for level 3 analyses, where multi-subject data are analyzed in group analyses.

Usage

setup_l3_models(
  gpa,
  l3_model_names = NULL,
  l2_model_names = NULL,
  l1_model_names = NULL
)

Arguments

gpa	a glm_pipeline_arguments object containing analysis speecification
l3_model_names	a subset of L3 models to be setup by this function. If not specified, all models in gpa$l2_models will be included
l2_model_names	a subset of L2 models to be setup by this function. If not specified, all models in gpa$l2_models will be included
l1_model_names	a subset of L1 models to be passed to L2 by this function. If not specified, all models in gpa$l1_models will be included

Details

This function will setup FSL level 2 (subject) .fsf files for all combinations of l2_model_names and l1_model_names.

FSL 2-level versus 3-level setup

2-level setup (one run per subject) - Pass L1 .feat folders as input to L3 .fsf setup - In this approach, the copes in the .fsf pertain to the L1 cope numbers - Requires one .fsf per L3 model

3-level setup (multiple runs per subject, combined at L2) - Pass individual cope*.feat folders within subject .gfeat folders - The folder cope numbers pertain to L1 copes - The cope*.nii.gz in the cope*.feat subfolders pertain to the L2 contrasts - Requires one .fsf per L1 cope x L3 model combination - Example: FSL_L2.gfeat/cope3.feat/stats/cope1.nii.gz ==> cope3 is the third contrast in the L1 feat model ==> cope1 is the first contrast in the L2 feat model

Author(s)

Michael Hallquist

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