Developers - API

Internal configuration system

A Python module to maintain unique, run-wide aslprep settings.

This module implements the memory structures to keep a consistent, singleton config. Settings are passed across processes via filesystem, and a copy of the settings for each run and subject is left under <output_dir>/sub-<participant_id>/log/<run_unique_id>/aslprep.toml. Settings are stored using ToML. The module has a to_filename() function to allow writting out the settings to hard disk in ToML format, which looks like:

This config file is used to pass the settings across processes, using the load() function.

Configuration sections

class environment

Read-only options regarding the platform and environment.

Crawls runtime descriptive settings (e.g., default FreeSurfer license, execution environment, nipype and aslprep versions, etc.). The environment section is not loaded in from file, only written out when settings are exported. This config section is useful when reporting issues, and these variables are tracked whenever the user does not opt-out using the --notrack argument.

cpu_count = 2

Number of available CPUs.

exec_docker_version = None

Version of Docker Engine.

exec_env = 'posix'

A string representing the execution platform.

free_mem = 3.4

Free memory at start.

nipype_version = '1.8.6'

Nipype’s current version.

overcommit_limit = '50%'

Linux’s kernel virtual memory overcommit limits.

overcommit_policy = 'heuristic'

Linux’s kernel virtual memory overcommit policy.

templateflow_version = '0.8.1'

The TemplateFlow client version installed.

version = '0.3.0'

aslprep’s version.

class execution

Configure run-level settings.

anat_derivatives = None

A path where anatomical derivatives are found to fast-track sMRIPrep.

bids_description_hash = None

Checksum (SHA256) of the dataset_description.json of the BIDS dataset.

bids_dir = None

An existing path to the dataset, which must be BIDS-compliant.

bids_filters = None

A dictionary of BIDS selection filters.

boilerplate_only = False

Only generate a boilerplate.

debug = False

Run in sloppy mode (meaning, suboptimal parameters that minimize run-time).

echo_idx = None

Select a particular echo for multi-echo EPI datasets.

fs_license_file = None

An existing file containing a FreeSurfer license.

fs_subjects_dir = None

FreeSurfer’s subjects directory.

classmethod init()

Create a new BIDS Layout accessible with layout.

layout = None

A BIDSLayout object, see init().

log_dir = None

The path to a directory that contains execution logs.

log_level = 25

Output verbosity.

low_mem = None

Utilize uncompressed NIfTIs and other tricks to minimize memory allocation.

md_only_boilerplate = False

Do not convert boilerplate from MarkDown to LaTex and HTML.

notrack = False

Do not monitor aslprep using Sentry.io.

output_dir = None

Folder where derivatives will be stored.

output_spaces = None

List of (non)standard spaces designated (with the --output-spaces flag of the command line) as spatial references for outputs.

participant_label = None

List of participant identifiers that are to be preprocessed.

reports_only = False

Only build the reports, based on the reportlets found in a cached working directory.

run_uuid = '20230407-180344_2b0e7821-ba41-44bb-88ba-664a6d7f135b'

Unique identifier of this particular run.

task_id = None

Select a particular task from all available in the dataset.

templateflow_home = PosixPath('/home/docs/.cache/templateflow')

The root folder of the TemplateFlow client.

work_dir = PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/aslprep/checkouts/0.3.0/docs/work')

Path to a working directory where intermediate results will be available.

write_graph = False

Write out the computational graph corresponding to the planned preprocessing.

class workflow

Configure the particular execution graph of this workflow.

anat_only = False

Execute the anatomical preprocessing only.

asl2t1w_dof = 6

Degrees of freedom of the ASL-to-T1w registration steps.

asl2t1w_init = 'register'

Whether to use standard coregistration (‘register’) or to initialize coregistration from the ASL image-header (‘header’).

basil = False

run BASIL, FSL utils to compute CBF with spatial regularilization and partial volume correction

dummy_vols = 0

pair for label-control volume to be deleted before cbf computation.

fmap_bspline = None

Regularize fieldmaps with a field of B-Spline basis.

fmap_demean = None

Remove the mean from fieldmaps.

force_syn = None

Run fieldmap-less susceptibility-derived distortions estimation.

hires = None

Run with the -hires flag.

ignore = None

Ignore particular steps for aslprep.

longitudinal = False

Run with the -logitudinal flag.

m0_scale = 1.0

relative scale between asl and M0.

random_seed = None

Master random seed to initialize the Pseudorandom Number Generator (PRNG)

scorescrub = False

run scorescrub, Sudipto’s alogrothims for denoisng CBF

skull_strip_fixed_seed = False

Fix a seed for skull-stripping.

skull_strip_t1w = 'force'

Skip brain extraction of the T1w image (default is force, meaning that aslprep will run brain extraction of the T1w).

skull_strip_template = 'OASIS30ANTs'

Change default brain extraction template.

smooth_kernel = 5.0

kernel size for smoothing M0.

spaces = None

Keeps the SpatialReferences instance keeping standard and nonstandard spaces.

use_bbr = None

Run boundary-based registration for ASL-to-T1w registration.

use_syn_sdc = None

Run fieldmap-less susceptibility-derived distortions estimation in the absence of any alternatives.

class nipype

Nipype settings.

crashfile_format = 'txt'

The file format for crashfiles, either text or pickle.

get_linked_libs = False

Run NiPype’s tool to enlist linked libraries for every interface.

classmethod get_plugin()

Format a dictionary for Nipype consumption.

classmethod init()

Set NiPype configurations.

memory_gb = None

Estimation in GB of the RAM this workflow can allocate at any given time.

nprocs = 2

Number of processes (compute tasks) that can be run in parallel (multiprocessing only).

omp_nthreads = None

Number of CPUs a single process can access for multithreaded execution.

plugin = 'MultiProc'

NiPype’s execution plugin.

plugin_args = {'maxtasksperchild': 1, 'raise_insufficient': False}

Settings for NiPype’s execution plugin.

resource_monitor = False

Enable resource monitor.

stop_on_first_crash = True

Whether the workflow should stop or continue after the first error.

Usage

A config file is used to pass settings and collect information as the execution graph is built across processes.

from aslprep import config
config_file = config.execution.work_dir / '.aslprep.toml'
config.to_filename(config_file)
# Call build_workflow(config_file, retval) in a subprocess
with Manager() as mgr:
    from aslprep.cli import build_workflow
    retval = mgr.dict()
    p = Process(target=build_workflow, args=(str(config_file), retval))
    p.start()
    p.join()
config.load(config_file)
# Access configs from any code section as:
value = config.section.setting

Logging

class loggers

Keep loggers easily accessible (see init()).

cli = <Logger cli (WARNING)>

Command-line interface logging.

default = <RootLogger root (WARNING)>

The root logger.

classmethod init()

Set the log level, initialize all loggers into loggers.

• Add new logger levels (25: IMPORTANT, and 15: VERBOSE).

• Add a new sub-logger (cli).

• Logger configuration.

interface = <Logger nipype.interface (INFO)>

NiPype’s interface logger.

utils = <Logger nipype.utils (INFO)>

NiPype’s utils logger.

workflow = <Logger nipype.workflow (INFO)>

NiPype’s workflow logger.

Other responsibilities

The config is responsible for other conveniency actions.

• Switching Python’s multiprocessing to forkserver mode.

• Set up a filter for warnings as early as possible.

• Automated I/O magic operations. Some conversions need to happen in the store/load processes (e.g., from/to Path <-> str, BIDSLayout, etc.)

dumps()

Format config into toml.

from_dict(settings)

Read settings from a flat dictionary.

get(flat=False)

Get config as a dict.

init_spaces(checkpoint=True)

Initialize the spaces setting.

load(filename)

Load settings from file.

to_filename(filename)

Write settings to file.

aslprep.workflows: Workflows

Nipype workflows for the ASLPrep BIDS App.

aslprep.workflows.base	ASLprep base processing workflows.
aslprep.workflows.asl.base	Preprocessing workflows for ASL data.
aslprep.workflows.asl.cbf	Workflows for calculating CBF.
aslprep.workflows.asl.confounds	Workflows for calculating confounds for ASL data.
aslprep.workflows.asl.ge_utils	Workflows to process GE ASL data.
aslprep.workflows.asl.gecbf	CBF-processing workflows for GE data.
aslprep.workflows.asl.hmc	Workflows for estimating and correcting head motion in ASL images.
aslprep.workflows.asl.outputs	Workflows for writing out derivative files.
aslprep.workflows.asl.plotting	Workflows for plotting ASLPrep derivatives.
aslprep.workflows.asl.qc	Workflows for calculating CBF QC metrics.
aslprep.workflows.asl.registration	Workflows for registering ASL data.
aslprep.workflows.asl.resampling	Workflows for resampling data.
aslprep.workflows.asl.stc	Slice-Timing Correction (STC) of ASL images.
aslprep.workflows.asl.t2s	Generate T2* map from multi-echo ASL images.

aslprep.interfaces: Interfaces

Nipype interfaces for aslprep.

aslprep.interfaces.ants	ANTS interfaces.
aslprep.interfaces.bids	Adapted interfaces from Niworkflows.
aslprep.interfaces.cbf_computation	Interfaces for calculating CBF.
aslprep.interfaces.confounds	Interfaces for calculating and collecting confounds.
aslprep.interfaces.ge	GE-specific interfaces.
aslprep.interfaces.multiecho	Interfaces for working with multi-echo data.
aslprep.interfaces.parcellation	Handling functional connectvity.
aslprep.interfaces.plotting	Plotting interfaces.
aslprep.interfaces.reports	Interfaces to generate reportlets.

aslprep.utils: Utilities

Utility functions for aslprep.

aslprep.utils.atlas	Functions for working with atlases.
aslprep.utils.bids	Utilities to handle BIDS inputs.
aslprep.utils.confounds	Functions for calculating and collecting confounds.
aslprep.utils.meepi	Multi-echo EPI utilities.
aslprep.utils.misc	Miscellaneous utilities.
aslprep.utils.plotting	Plotting functions and classes.
aslprep.utils.qc	Functions for evaluating quality of ASL derivatives.
aslprep.utils.sentry	Stripped out routines for Sentry.