afni_3dfwhmx: R6 class for running 3dFWHMx on a single input file based on...

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

R6 class for running 3dFWHMx on a single input file based on user specification

Description

R6 class for running 3dFWHMx on a single input file based on user specification

R6 class for running 3dFWHMx on a single input file based on user specification

Details

N.B. This class doesn't even expose the Gaussian ACF options given false positive problems

Methods

Public methods

• afni_3dfwhmx$new()

• afni_3dfwhmx$run()

• afni_3dfwhmx$get_call()

• afni_3dfwhmx$get_acf_params()

• afni_3dfwhmx$get_acf_by_radius()

• afni_3dfwhmx$get_fwhm_by_volume()

• afni_3dfwhmx$get_input_file()

• afni_3dfwhmx$get_mask_file()

• afni_3dfwhmx$get_outputs()

• afni_3dfwhmx$is_complete()

• afni_3dfwhmx$delete_outputs()

• afni_3dfwhmx$clone()

---

Method new()

Usage

afni_3dfwhmx$new(
  input_file = NULL,
  mask_file = NULL,
  out_dir = NULL,
  demed = NULL,
  unif = NULL,
  average = "geometric",
  ncpus = 1L
)

Arguments

input_file

The input dataset whose smoothness should be calculated (often first-level GLM residuals)

mask_file

Only compute smoothness within this mask (if not provided, -automask will be used)

out_dir

The output directory for fwhmx files

demed

If TRUE, subtract the median of each voxels time series before calculating FWHM (wraps -demed). Default: FALSE.

unif

If TRUE, normalize each voxel's time series to have the same MAD before calculating FWHM (wraps -unif). Default: FALSE

average

For multi-volume data, compute the averaged ACF estimates by either the geometric or arithmetic mean. Default: "geometric".

ncpus

The number of threads/cores to use for running 3dFWHMx. Default is 1. Controls OMP_NUM_THREADS.

---

Method run()

runs 3dFWHMx on this input dataset

Usage

afni_3dfwhmx$run(force = FALSE)

Arguments

force

If TRUE, 3dFWHMx will be run even if the expected output files already exist.

---

Method get_call()

return the 3dFWHMx call used for the specified input

Usage

afni_3dfwhmx$get_call()

Details

this is useful if you want to call 3dFWHMx yourself directly or if you want to debug the 3dFWHMx call specification.

Returns

a character string with the 3dFWHMx call

---

Method get_acf_params()

return the estimated ACF parameters for this run of data, averaged over volumes

Usage

afni_3dfwhmx$get_acf_params()

Details

Will issue a warning if 3dFWHMx has not run successfully on this dataset already

Returns

a three-element vector containing the ACF estimates for the dataset, averaging over volumes.

---

Method get_acf_by_radius()

return the estimated ACF parameters for this run of data

Usage

afni_3dfwhmx$get_acf_by_radius()

Details

Will issue a warning if 3dFWHMx has not run successfully on this dataset already

Returns

a three-element vector containing the ACF estimates for the dataset, averaging over volumes.

---

Method get_fwhm_by_volume()

return the estimated ACF parameters for this run of data

Usage

afni_3dfwhmx$get_fwhm_by_volume()

Details

Will issue a warning if 3dFWHMx has not run successfully on this dataset already

Returns

a three-element vector containing the ACF estimates for the dataset, averaging over volumes.

---

Method get_input_file()

return the input file (NIfTI) used for 3dFWHMx

Usage

afni_3dfwhmx$get_input_file()

Returns

a character string of the input file location

---

Method get_mask_file()

return the mask file used for 3dFWHMx estimation

Usage

afni_3dfwhmx$get_mask_file()

Returns

a character string of the mask file location

---

Method get_outputs()

return the expected output files related to this 3dFWHMx object

Usage

afni_3dfwhmx$get_outputs()

Returns

a character vector containing expected output files

---

Method is_complete()

method to indicate whether 3dFWHMx has already run and completed for this input

Usage

afni_3dfwhmx$is_complete()

Returns

TRUE if expected 3dFWHMx output file exists, FALSE if it does not

---

Method delete_outputs()

method to delete any/all files generated by this object

Usage

afni_3dfwhmx$delete_outputs(prompt = FALSE)

Arguments

prompt

if TRUE, user will have to confirm deletion of each file. If FALSE, files are deleted without prompting.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

afni_3dfwhmx$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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