afni_3dfwhmx_list: R6 class for running 3dFWHMx on a group of input files using...

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

R6 class for running 3dFWHMx on a group of input files using a scheduler/cluster

Description

R6 class for running 3dFWHMx on a group of input files using a scheduler/cluster

R6 class for running 3dFWHMx on a group of input files using a scheduler/cluster

Methods

Public methods

• afni_3dfwhmx_list$new()

• afni_3dfwhmx_list$refresh()

• afni_3dfwhmx_list$submit()

• afni_3dfwhmx_list$get_batch()

• afni_3dfwhmx_list$get_acf_average()

• afni_3dfwhmx_list$get_acf_df()

• afni_3dfwhmx_list$get_effective_fwhm()

• afni_3dfwhmx_list$is_complete()

• afni_3dfwhmx_list$clone()

---

Method new()

create a new afni_3dfwhmx_list object

Usage

afni_3dfwhmx_list$new(
  input_files = NULL,
  mask_files = NULL,
  scheduler = NULL,
  wall_time = "10:00:00"
)

Arguments

input_files

A vector of input files that should each be passed to 3dFWHMx (usually first-level residuals)

mask_files

A vector of mask files corresponding to input_files (i.e., these should align), use to set the volume over which smoothness is estimated by 3dFWHMx

scheduler

The HPC scheduler to be used: 'local', 'slurm', or 'torque'. Default: 'slurm'

wall_time

The total time required to run all 3dFWHMx objects on the job scheduler/HPC

---

Method refresh()

recreate afni_3dfwhmx objects and completion status

Usage

afni_3dfwhmx_list$refresh(...)

Arguments

...

Passes through any arguments to afni_3dfwhmx$new()

Details

useful for updating job status and ACF params after a run completes

---

Method submit()

Submit the 3dFWHMx batch for all inputs to the scheduler

Usage

afni_3dfwhmx_list$submit(force = FALSE)

Arguments

force

If TRUE, completed 3dFWHMx runs will be included in the batch. Default: FALSE

---

Method get_batch()

Return R_batch_job objects used to submit 3dFWHMx for all inputs

Usage

afni_3dfwhmx_list$get_batch(include_complete = FALSE)

Arguments

include_complete

If TRUE, complete 3dFWHMx jobs will be included in the batch, leading these to be re-run

---

Method get_acf_average()

method to calculate the overall ACF average across all input datasets

Usage

afni_3dfwhmx_list$get_acf_average(allow_incomplete_fwhmx = FALSE)

Arguments

allow_incomplete_fwhmx

If TRUE, the average will be calculated even if some datasets do not have 3dFWHMx parameter estimates (e.g., if they crashed or were never run). Default. FALSE.

Returns

a three-element vector containing the ACF estimates averaged across all datasets

---

Method get_acf_df()

return the 3dFWHMx results as a data.frame

Usage

afni_3dfwhmx_list$get_acf_df()

---

Method get_effective_fwhm()

return the effective FWHM estimated by 3dFWHMx -ACF

Usage

afni_3dfwhmx_list$get_effective_fwhm()

---

Method is_complete()

Simple method to return whether 3dFWHMx is complete for all input files

Usage

afni_3dfwhmx_list$is_complete()

Returns

returns TRUE if 3dFWHMx has completed for all runs

---

Method clone()

The objects of this class are cloneable with this method.

Usage

afni_3dfwhmx_list$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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