combine_feat_l3_to_afni: Function to combine Feat L3 analyses into AFNI BRIK+HEAD...

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

Function to combine Feat L3 analyses into AFNI BRIK+HEAD files according to user-specified combinations

Description

Function to combine Feat L3 analyses into AFNI BRIK+HEAD files according to user-specified combinations

Usage

combine_feat_l3_to_afni(
  gpa,
  feat_l3_combined_filename = NULL,
  feat_l3_combined_briknames = NULL,
  template_brain = NULL
)

Arguments

gpa	a glm_pipeline_arguments object having a populated l3_model_setup field. The L3 analyses should also be complete (i.e., after run_glm_pipeline).
feat_l3_combined_filename	a glue expression for the path and filename prefix
feat_l3_combined_briknames	a glue expression for naming the subbriks in the AFNI output
template_brain	an optional filename for the MNI template that should be used as an underlay in AFNI. This image will be symbolically linked into each directory created by combine_feat_l3_to_afni.

Details

To specify the folder and filename structure for the combined feat analyses, use a glue expression that indicates how outputs should be structured. In particular, variables in gpa$l3_model_setup$fsl can be used for dynamically naming of afni outputs.

l1_model

the name of the level 1 model

l2_model

the name of the level 2 model

l3_model

the name of the level 3 model

l1_cope_name

the level 1 contrast name

l2_cope_name

the level 2 contrast name

l3_cope_name

the level 3 contrast name

Examples

## Not run: 
  feat_l3_combined_filename <- "{gpa$output_directory}/afni_combined/L1m-{l1_model}/l1c-{l1_cope_name}/L3m-{l3_model}_stats"
  feat_l3_combined_briknames = "l2c-{l2_cope_name}_l3c-{l3_cope_name}"
  template_brain <- "/proj/mnhallqlab/lab_resources/standard/mni_icbm152_nlin_asym_09c/mni_icbm152_t1_tal_nlin_asym_09c_brain.nii"

  combine_feat_l3_to_afni(gpa, feat_l3_combined_filename, feat_l3_combined_briknames, template_brain)

## End(Not run)

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