simulate_null_3dttest: helper class to generate 3dttest++ null datasets using...

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

helper class to generate 3dttest++ null datasets using -randomsign

Description

helper class to generate 3dttest++ null datasets using -randomsign

helper class to generate 3dttest++ null datasets using -randomsign

Methods

Public methods

• simulate_null_3dttest$new()

• simulate_null_3dttest$is_complete()

• simulate_null_3dttest$submit()

• simulate_null_3dttest$get_3dttest_calls()

• simulate_null_3dttest$get_permutation_files()

• simulate_null_3dttest$get_batch()

• simulate_null_3dttest$get_use_sdat()

• simulate_null_3dttest$clone()

---

Method new()

initialize a simulate_null_3dttest object to support 3dttest++ -randomsign

Usage

simulate_null_3dttest$new(
  residuals_file = NULL,
  mask_file = NULL,
  njobs = NULL,
  n_permutations = NULL,
  use_sdat = NULL,
  wall_time = NULL,
  memgb_per_3dttest = NULL,
  memgb_combine = NULL
)

Arguments

residuals_file

the 4D file containing voxelwise residuals for all subjects (e.g., res4d.nii.gz in FEAT)

mask_file

A mask file used to specify which voxels should be analyzed/permuted

njobs

The number of independent jobs across which permutations are distributed

n_permutations

The total number of null datasets to be computed by sign-flipping

use_sdat

a logical indicating whether to output null datasets in sdat format (single-precision, serialized, I think)

wall_time

The amount of compute time needed for this job as a dd-hh:mm:ss string

memgb_per_3dttest

The number of gigabytes of memory requested for each 3dttest++ permutation process. If not specified, 8 will be requested

memgb_combine

The number of gigabytes of memory requested for the parent 3dttest++ job that combines permutation outputs. If not specified, 32 will be requested

---

Method is_complete()

test whether the expected outputs of the permutation are complete

Usage

simulate_null_3dttest$is_complete()

Returns

a boolean indicating whether the expected output file exists

---

Method submit()

submit the permutation job to the cluster

Usage

simulate_null_3dttest$submit(force = FALSE)

Arguments

force

whether to run the permutation job even if the outputs are already complete method to return R_batch_job to run 3dttest permutations

---

Method get_3dttest_calls()

Usage

simulate_null_3dttest$get_3dttest_calls(include_complete = FALSE)

---

Method get_permutation_files()

Usage

simulate_null_3dttest$get_permutation_files()

---

Method get_batch()

Usage

simulate_null_3dttest$get_batch()

---

Method get_use_sdat()

Usage

simulate_null_3dttest$get_use_sdat()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

simulate_null_3dttest$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

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