diff --git a/src/fmripost_aroma/cli/parser.py b/src/fmripost_aroma/cli/parser.py index aa272c2..28cade6 100644 --- a/src/fmripost_aroma/cli/parser.py +++ b/src/fmripost_aroma/cli/parser.py @@ -21,6 +21,7 @@ # https://www.nipreps.org/community/licensing/ # """Parser.""" + import sys from fmripost_aroma import config @@ -31,6 +32,7 @@ def _build_parser(**kwargs): ``kwargs`` are passed to ``argparse.ArgumentParser`` (mainly useful for debugging). """ + from argparse import Action, ArgumentDefaultsHelpFormatter, ArgumentParser from functools import partial from pathlib import Path @@ -464,6 +466,7 @@ def _bids_filter(value, parser): def parse_args(args=None, namespace=None): """Parse args and run further checks on the command line.""" + import logging parser = _build_parser() diff --git a/src/fmripost_aroma/cli/run.py b/src/fmripost_aroma/cli/run.py index eb92659..ebeaeb9 100644 --- a/src/fmripost_aroma/cli/run.py +++ b/src/fmripost_aroma/cli/run.py @@ -22,6 +22,7 @@ # https://www.nipreps.org/community/licensing/ # """fMRI preprocessing workflow.""" + from fmripost_aroma import config EXITCODE: int = -1 @@ -29,6 +30,7 @@ def main(): """Entry point.""" + import gc import sys from multiprocessing import Manager, Process diff --git a/src/fmripost_aroma/config.py b/src/fmripost_aroma/config.py index eae2ac3..8615933 100644 --- a/src/fmripost_aroma/config.py +++ b/src/fmripost_aroma/config.py @@ -87,6 +87,7 @@ :py:class:`~bids.layout.BIDSLayout`, etc.) """ + import os from multiprocessing import set_start_method diff --git a/src/fmripost_aroma/workflows/aroma.py b/src/fmripost_aroma/workflows/aroma.py index 722721c..e3d58f0 100644 --- a/src/fmripost_aroma/workflows/aroma.py +++ b/src/fmripost_aroma/workflows/aroma.py @@ -21,6 +21,7 @@ # https://www.nipreps.org/community/licensing/ # """fMRIPost-AROMA workflows to run ICA-AROMA.""" + import os from nipype.interfaces import utility as niu @@ -124,6 +125,7 @@ def init_ica_aroma_wf( nonaggr_denoised_file BOLD series with non-aggressive ICA-AROMA denoising applied """ + from nipype.interfaces import fsl from niworkflows.engine.workflows import LiterateWorkflow as Workflow from niworkflows.interfaces.utility import TSV2JSON @@ -137,7 +139,7 @@ def init_ica_aroma_wf( [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space* time-series after removal of non-steady state volumes and spatial smoothing with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum). -Corresponding "non-aggresively" denoised runs were produced after such +Corresponding "non-aggressively" denoised runs were produced after such smoothing. Additionally, the "aggressive" noise-regressors were collected and placed in the corresponding confounds file. diff --git a/src/fmripost_aroma/workflows/base.py b/src/fmripost_aroma/workflows/base.py index 8e4d5de..de31dfe 100644 --- a/src/fmripost_aroma/workflows/base.py +++ b/src/fmripost_aroma/workflows/base.py @@ -28,6 +28,7 @@ .. autofunction:: init_single_subject_wf """ + import os import sys import warnings