dmriprep.config package¶

A Python module to maintain unique, run-wide dMRIPrep 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>/dmriprep.toml. Settings are stored using ToML. The module has a to_filename() function to allow writing out the settings to hard disk in ToML format, which looks like:

Example file representation of dMRIPrep settings.¶

[environment]
cpu_count = 8
exec_env = "posix"
free_mem = 1.0
overcommit_policy = "heuristic"
overcommit_limit = "50%"
nipype_version = "1.4.2"
templateflow_version = "0.4.2"
version = "0.2.2"

[execution]
bids_dir = "THP002/"
bids_description_hash = "b07ee615a588acf67967d70f5b2402ffbe477b99a316433fa7fdaff4f9dad5c1"
boilerplate_only = false
debug = false
fs_license_file = "/opt/freesurfer/license.txt"
fs_subjects_dir = "opt/freesurfer/subjects"
layout = "BIDS Layout: .../home/oesteban/Data/THP002 | Subjects: 1 | Sessions: 2 | Runs: 2"
log_dir = "/tmp/dmriprep/logs"
log_level = 40
low_mem = false
md_only_boilerplate = false
notrack = true
output_dir = "/tmp"
output_spaces = "run"
reports_only = false
run_uuid = "20200311-121754_aa0b4fa9-6b60-4a11-af7d-02deb54a823f"
participant_label = [ "THP0005",]
templateflow_home = "/usr/share/templateflow"
work_dir = "work/"
write_graph = false

[workflow]
anat_only = false
fmap_bspline = false
force_syn = false
hires = true
ignore = []
longitudinal = false
run_reconall = true
skull_strip_fixed_seed = false
skull_strip_template = "OASIS30ANTs"
spaces = "run"

[nipype]
crashfile_format = "txt"
get_linked_libs = false
nprocs = 8
omp_nthreads = 8
plugin = "MultiProc"
resource_monitor = false
stop_on_first_crash = false

[nipype.plugin_args]
maxtasksperchild = 1
raise_insufficient = false

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

Configuration sections¶

class dmriprep.config.environment¶

Read-only options regarding the platform and environment.

Crawls runtime descriptive settings (e.g., default FreeSurfer license, execution environment, nipype and dMRIPrep 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 = 36¶: Number of available CPUs.

exec_docker_version = None¶: Version of Docker Engine.

exec_env = 'posix'¶: A string representing the execution platform.

free_mem = None¶: Free memory at start.

nipype_version = '1.5.1'¶: 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 = '0.7.1'¶: The TemplateFlow client version installed.

version = '0.5.0+30.g510ed0ea'¶: dMRIPrep’s version.

class dmriprep.config.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).

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 dMRIPrep using Google Analytics.

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 = '20210907-144350_81c1a74d-fb34-4268-83ec-3ca6ffed527e'¶: Unique identifier of this particular run.

templateflow_home = PosixPath('/root/.cache/templateflow')¶: The root folder of the TemplateFlow client.

work_dir = PosixPath('/root/project/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 dmriprep.config.workflow¶

Configure the particular execution graph of this workflow.

anat_only = False¶: Execute the anatomical preprocessing only.

dwi2t1w_init = 'register'¶: Whether to use standard coregistration (‘register’) or to initialize coregistration from the DWI header (‘header’).

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 FreeSurfer recon-all with the -hires flag.

ignore = None¶: Ignore particular steps for dMRIPrep.

longitudinal = False¶: Run FreeSurfer recon-all with the -logitudinal flag.

run_reconall = True¶: Run FreeSurfer’s surface reconstruction.

skull_strip_fixed_seed = False¶: Fix a seed for skull-stripping.

skull_strip_template = 'OASIS30ANTs'¶: Change default brain extraction template.

spaces = None¶: Keeps the SpatialReferences instance keeping standard and nonstandard spaces.

use_syn = None¶: Run fieldmap-less susceptibility-derived distortions estimation in the absence of any alternatives.

class dmriprep.config.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 = 36¶: Number of processes (compute tasks) that can be run in parallel (multiprocessing only).

omp_nthreads = 36¶: Number of CPUs a single process can access for multithreaded execution.

parameterize_dirs = False¶: The node’s output directory will contain full parameterization of any iterable, otherwise parameterizations over 32 characters will be replaced by their hash.

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 dmriprep import config
config_file = config.execution.work_dir / '.dmriprep.toml'
config.to_filename(config_file)
# Call build_workflow(config_file, retval) in a subprocess
with Manager() as mgr:
    from .workflow 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 dmriprep.config.loggers¶

Keep loggers easily accessible (see init()).

cli = <Logger cli (DEBUG)>¶: Command-line interface logging.

default = <RootLogger root (DEBUG)>¶: 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 convenience 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.)

dmriprep.config.dumps(flat=False)¶: Format config into toml.

class dmriprep.config.environment

Bases: dmriprep.config._Config

Read-only options regarding the platform and environment.

Crawls runtime descriptive settings (e.g., default FreeSurfer license, execution environment, nipype and dMRIPrep 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 = 36: Number of available CPUs.

exec_docker_version = None: Version of Docker Engine.

exec_env = 'posix': A string representing the execution platform.

free_mem = None: Free memory at start.

nipype_version = '1.5.1': 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 = '0.7.1': The TemplateFlow client version installed.

version = '0.5.0+30.g510ed0ea': dMRIPrep’s version.

class dmriprep.config.execution

Bases: dmriprep.config._Config

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).

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 dMRIPrep using Google Analytics.

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 = '20210907-144350_81c1a74d-fb34-4268-83ec-3ca6ffed527e': Unique identifier of this particular run.

templateflow_home = PosixPath('/root/.cache/templateflow'): The root folder of the TemplateFlow client.

work_dir = PosixPath('/root/project/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.

dmriprep.config.from_dict(settings)¶: Read settings from a flat dictionary.

dmriprep.config.get(flat=False)¶: Get config as a dict.

dmriprep.config.init_spaces(checkpoint=True)¶: Initialize the spaces setting.

dmriprep.config.load(filename)¶: Load settings from file.

class dmriprep.config.loggers

Bases: object

Keep loggers easily accessible (see init()).

cli = <Logger cli (DEBUG)>: Command-line interface logging.

default = <RootLogger root (DEBUG)>: 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.

class dmriprep.config.nipype

Bases: dmriprep.config._Config

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 = 36: Number of processes (compute tasks) that can be run in parallel (multiprocessing only).

omp_nthreads = 36: Number of CPUs a single process can access for multithreaded execution.

parameterize_dirs = False: The node’s output directory will contain full parameterization of any iterable, otherwise parameterizations over 32 characters will be replaced by their hash.

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.

dmriprep.config.redirect_warnings(message, category, filename, lineno, file=None, line=None)¶: Redirect other warnings.

dmriprep.config.to_filename(filename)¶: Write settings to file.

class dmriprep.config.workflow

Bases: dmriprep.config._Config

Configure the particular execution graph of this workflow.

anat_only = False: Execute the anatomical preprocessing only.

dwi2t1w_init = 'register': Whether to use standard coregistration (‘register’) or to initialize coregistration from the DWI header (‘header’).

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 FreeSurfer recon-all with the -hires flag.

ignore = None: Ignore particular steps for dMRIPrep.

longitudinal = False: Run FreeSurfer recon-all with the -logitudinal flag.

run_reconall = True: Run FreeSurfer’s surface reconstruction.

skull_strip_fixed_seed = False: Fix a seed for skull-stripping.

skull_strip_template = 'OASIS30ANTs': Change default brain extraction template.

spaces = None: Keeps the SpatialReferences instance keeping standard and nonstandard spaces.

use_syn = None: Run fieldmap-less susceptibility-derived distortions estimation in the absence of any alternatives.