From 203f1c9e0470a5b833b62c9314db2cbc1478dfc9 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 8 Feb 2020 15:09:50 -0800
Subject: [PATCH 01/43] WIP/ENH: Config file and BIDSLayout index

---
 fmriprep/cli/parser.py                  | 418 ++++++++++++++
 fmriprep/cli/run.py                     | 725 +++---------------------
 fmriprep/cli/tests/test_parser.py       |  68 +++
 fmriprep/cli/workflow.py                | 122 ++++
 fmriprep/config.py                      | 358 +++++++++++-
 fmriprep/utils/bids.py                  |   8 +-
 fmriprep/utils/meepi.py                 |   8 +-
 fmriprep/utils/misc.py                  |  13 +
 fmriprep/utils/sentry.py                |  25 +-
 fmriprep/utils/testing.py               |   2 -
 fmriprep/workflows/base.py              | 503 ++--------------
 fmriprep/workflows/bold/base.py         | 188 ++----
 fmriprep/workflows/bold/registration.py |   4 +-
 fmriprep/workflows/bold/stc.py          |   4 +-
 fmriprep/workflows/bold/t2s.py          |   5 +-
 setup.cfg                               |   2 +-
 16 files changed, 1178 insertions(+), 1275 deletions(-)
 create mode 100644 fmriprep/cli/parser.py
 create mode 100644 fmriprep/cli/tests/test_parser.py
 create mode 100644 fmriprep/cli/workflow.py
 create mode 100644 fmriprep/utils/misc.py

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
new file mode 100644
index 000000000..fafdc6936
--- /dev/null
+++ b/fmriprep/cli/parser.py
@@ -0,0 +1,418 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Parser."""
+import os
+from .. import config
+
+
+def _build_parser():
+    """Build parser object."""
+    from functools import partial
+    from pathlib import Path
+    from argparse import (
+        ArgumentParser,
+        ArgumentDefaultsHelpFormatter,
+    )
+    from packaging.version import Version
+    from .version import check_latest, is_flagged
+    from niworkflows.utils.spaces import Reference, SpatialReferences, OutputReferencesAction
+
+    def _path_exists(path, parser):
+        """Ensure a given path exists."""
+        if path is None or not Path(path).exists():
+            raise parser.error("Path does not exist: <%s>." % path)
+        return Path(path).absolute()
+
+    def _min_one(value, parser):
+        """Ensure an argument is not lower than 1."""
+        value = int(value)
+        if value < 1:
+            raise parser.error("Argument can't be less than one.")
+        return value
+
+    def _to_gb(value):
+        scale = {"G": 1, "T": 10**3, "M": 1e-3, "K": 1e-6, "B": 1e-9}
+        digits = ''.join([c for c in value if c.isdigit()])
+        units = value[len(digits):] or "M"
+        return int(digits) * scale[units[0]]
+
+    def _drop_sub(value):
+        value = str(value)
+        return value.lstrip('sub-')
+
+    def _bids_filter(value):
+        from json import loads
+        if value and Path(value).exists():
+            return loads(Path(value).read_text())
+
+    verstr = 'fMRIPrep v{}'.format(config.execution.version)
+    currentv = Version(config.execution.version)
+    is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
+
+    parser = ArgumentParser(
+        description='fMRIPrep: fMRI PREProcessing workflows v{}'.format(config.execution.version),
+        formatter_class=ArgumentDefaultsHelpFormatter)
+    PathExists = partial(_path_exists, parser=parser)
+    PositiveInt = partial(_min_one, parser=parser)
+
+    # Arguments as specified by BIDS-Apps
+    # required, positional arguments
+    # IMPORTANT: they must go directly with the parser object
+    parser.add_argument('bids_dir', action='store', type=PathExists,
+                        help='the root folder of a BIDS valid dataset (sub-XXXXX folders should '
+                             'be found at the top level in this folder).')
+    parser.add_argument('output_dir', action='store', type=Path,
+                        help='the output path for the outcomes of preprocessing and visual '
+                             'reports')
+    parser.add_argument('analysis_level', choices=['participant'],
+                        help='processing stage to be run, only "participant" in the case of '
+                             'fMRIPrep (see BIDS-Apps specification).')
+
+    # optional arguments
+    parser.add_argument('--version', action='version', version=verstr)
+
+    g_bids = parser.add_argument_group('Options for filtering BIDS queries')
+    g_bids.add_argument('--skip_bids_validation', '--skip-bids-validation', action='store_true',
+                        default=False,
+                        help='assume the input dataset is BIDS compliant and skip the validation')
+    g_bids.add_argument(
+        '--participant-label', '--participant_label', action='store', nargs='+', type=_drop_sub,
+        help='a space delimited list of participant identifiers or a single '
+             'identifier (the sub- prefix can be removed)')
+    # Re-enable when option is actually implemented
+    # g_bids.add_argument('-s', '--session-id', action='store', default='single_session',
+    #                     help='select a specific session to be processed')
+    # Re-enable when option is actually implemented
+    # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
+    #                     help='select a specific run to be processed')
+    g_bids.add_argument('-t', '--task-id', action='store',
+                        help='select a specific task to be processed')
+    g_bids.add_argument('--echo-idx', action='store', type=int,
+                        help='select a specific echo to be processed in a multiecho series')
+    g_bids.add_argument(
+        '--bids-filter-file', dest='bids_filters', action='store',
+        type=_bids_filter, metavar='PATH',
+        help='a JSON file describing custom BIDS input filter using pybids '
+             '{<suffix>:{<entity>:<filter>,...},...} '
+             '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)')
+
+    g_perfm = parser.add_argument_group('Options to handle performance')
+    g_perfm.add_argument(
+        '--nprocs', '--nthreads', '--n_cpus', '-n-cpus', action='store', type=PositiveInt,
+        help='maximum number of threads across all processes')
+    g_perfm.add_argument('--omp-nthreads', action='store', type=PositiveInt,
+                         help='maximum number of threads per-process')
+    g_perfm.add_argument('--mem', '--mem_mb', '--mem-mb', dest='memory_gb',
+                         action='store', type=_to_gb,
+                         help='upper bound memory limit for fMRIPrep processes')
+    g_perfm.add_argument('--low-mem', action='store_true',
+                         help='attempt to reduce memory usage (will increase disk usage '
+                              'in working directory)')
+    g_perfm.add_argument('--use-plugin', action='store', default=None,
+                         help='nipype plugin configuration file')
+    g_perfm.add_argument('--anat-only', action='store_true',
+                         help='run anatomical workflows only')
+    g_perfm.add_argument('--boilerplate_only', action='store_true', default=False,
+                         help='generate boilerplate only')
+    g_perfm.add_argument('--md-only-boilerplate', action='store_true',
+                         default=False,
+                         help='skip generation of HTML and LaTeX formatted citation with pandoc')
+    g_perfm.add_argument('--error-on-aroma-warnings', action='store_true',
+                         dest='aroma_err_on_warn', default=False,
+                         help='Raise an error if ICA_AROMA does not produce sensible output '
+                              '(e.g., if all the components are classified as signal or noise)')
+    g_perfm.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
+                         help="increases log verbosity for each occurence, debug level is -vvv")
+
+    g_conf = parser.add_argument_group('Workflow configuration')
+    g_conf.add_argument(
+        '--ignore', required=False, action='store', nargs="+", default=[],
+        choices=['fieldmaps', 'slicetiming', 'sbref'],
+        help='ignore selected aspects of the input dataset to disable corresponding '
+             'parts of the workflow (a space delimited list)')
+    g_conf.add_argument(
+        '--longitudinal', action='store_true',
+        help='treat dataset as longitudinal - may increase runtime')
+    g_conf.add_argument(
+        '--t2s-coreg', action='store_true',
+        help='If provided with multi-echo BOLD dataset, create T2*-map and perform '
+             'T2*-driven coregistration. When multi-echo data is provided and this '
+             'option is not enabled, standard EPI-T1 coregistration is performed '
+             'using the middle echo.')
+    g_conf.add_argument(
+        '--output-spaces', nargs='+', action=OutputReferencesAction, default=SpatialReferences(),
+        help="""\
+Standard and non-standard spaces to resample anatomical and functional images to. \
+Standard spaces may be specified by the form \
+``<SPACE>[:cohort-<label>][:res-<resolution>][...]``, where ``<SPACE>`` is \
+a keyword designating a spatial reference, and may be followed by optional, \
+colon-separated parameters. \
+Non-standard spaces imply specific orientations and sampling grids. \
+Important to note, the ``res-*`` modifier does not define the resolution used for \
+the spatial normalization.
+For further details, please check out \
+https://fmriprep.readthedocs.io/en/%s/spaces.html""" % (currentv.base_version
+                                                        if is_release else 'latest'))
+
+    g_conf.add_argument('--bold2t1w-dof', action='store', default=6, choices=[6, 9, 12], type=int,
+                        help='Degrees of freedom when registering BOLD to T1w images. '
+                             '6 degrees (rotation and translation) are used by default.')
+    g_conf.add_argument(
+        '--force-bbr', action='store_true', dest='use_bbr', default=None,
+        help='Always use boundary-based registration (no goodness-of-fit checks)')
+    g_conf.add_argument(
+        '--force-no-bbr', action='store_false', dest='use_bbr', default=None,
+        help='Do not use boundary-based registration (no goodness-of-fit checks)')
+    g_conf.add_argument(
+        '--medial-surface-nan', required=False, action='store_true', default=False,
+        help='Replace medial wall values with NaNs on functional GIFTI files. Only '
+        'performed for GIFTI files mapped to a freesurfer subject (fsaverage or fsnative).')
+    g_conf.add_argument(
+        '--dummy-scans', required=False, action='store', default=None, type=int,
+        help='Number of non steady state volumes.')
+
+    # ICA_AROMA options
+    g_aroma = parser.add_argument_group('Specific options for running ICA_AROMA')
+    g_aroma.add_argument('--use-aroma', action='store_true', default=False,
+                         help='add ICA_AROMA to your preprocessing stream')
+    g_aroma.add_argument('--aroma-melodic-dimensionality', dest='aroma_melodic_dim',
+                         action='store', default=-200, type=int,
+                         help='Exact or maximum number of MELODIC components to estimate '
+                         '(positive = exact, negative = maximum)')
+
+    # Confounds options
+    g_confounds = parser.add_argument_group('Specific options for estimating confounds')
+    g_confounds.add_argument(
+        '--return-all-components', required=False, action='store_true', default=False,
+        help='Include all components estimated in CompCor decomposition in the confounds '
+             'file instead of only the components sufficient to explain 50 percent of '
+             'BOLD variance in each CompCor mask')
+    g_confounds.add_argument(
+        '--fd-spike-threshold', required=False, action='store', default=0.5, type=float,
+        help='Threshold for flagging a frame as an outlier on the basis of framewise '
+             'displacement')
+    g_confounds.add_argument(
+        '--dvars-spike-threshold', required=False, action='store', default=1.5, type=float,
+        help='Threshold for flagging a frame as an outlier on the basis of standardised '
+             'DVARS')
+
+    #  ANTs options
+    g_ants = parser.add_argument_group('Specific options for ANTs registrations')
+    g_ants.add_argument(
+        '--skull-strip-template', default='OASIS30ANTs', type=Reference.from_string,
+        help='select a template for skull-stripping with antsBrainExtraction')
+    g_ants.add_argument('--skull-strip-fixed-seed', action='store_true',
+                        help='do not use a random seed for skull-stripping - will ensure '
+                             'run-to-run replicability when used with --omp-nthreads 1')
+
+    # Fieldmap options
+    g_fmap = parser.add_argument_group('Specific options for handling fieldmaps')
+    g_fmap.add_argument('--fmap-bspline', action='store_true', default=False,
+                        help='fit a B-Spline field using least-squares (experimental)')
+    g_fmap.add_argument('--fmap-no-demean', action='store_false', default=True,
+                        help='do not remove median (within mask) from fieldmap')
+
+    # SyN-unwarp options
+    g_syn = parser.add_argument_group('Specific options for SyN distortion correction')
+    g_syn.add_argument('--use-syn-sdc', action='store_true', default=False,
+                       help='EXPERIMENTAL: Use fieldmap-free distortion correction')
+    g_syn.add_argument('--force-syn', action='store_true', default=False,
+                       help='EXPERIMENTAL/TEMPORARY: Use SyN correction in addition to '
+                       'fieldmap correction, if available')
+
+    # FreeSurfer options
+    g_fs = parser.add_argument_group('Specific options for FreeSurfer preprocessing')
+    g_fs.add_argument(
+        '--fs-license-file', metavar='PATH', type=PathExists,
+        help='Path to FreeSurfer license key file. Get it (for free) by registering'
+             ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
+    g_fs.add_argument(
+        '--fs-subjects-dir', metavar='PATH', type=Path,
+        help='Path to existing FreeSurfer subjects directory to reuse. '
+             '(default: OUTPUT_DIR/freesurfer)')
+
+    # Surface generation xor
+    g_surfs = parser.add_argument_group('Surface preprocessing options')
+    g_surfs.add_argument('--no-submm-recon', action='store_false', dest='hires',
+                         help='disable sub-millimeter (hires) reconstruction')
+    g_surfs_xor = g_surfs.add_mutually_exclusive_group()
+    g_surfs_xor.add_argument('--cifti-output', nargs='?', const='91k', default=False,
+                             choices=('91k', '170k'), type=str,
+                             help='output preprocessed BOLD as a CIFTI dense timeseries. '
+                             'Optionally, the number of grayordinate can be specified '
+                             '(default is 91k, which equates to 2mm resolution)')
+    g_surfs_xor.add_argument('--fs-no-reconall',
+                             action='store_false', dest='run_reconall',
+                             help='disable FreeSurfer surface preprocessing.')
+
+    g_other = parser.add_argument_group('Other options')
+    g_other.add_argument(
+        '-w', '--work-dir', action='store', type=Path, default=Path('work').absolute(),
+        help='path where intermediate results should be stored')
+    g_other.add_argument('--clean-workdir', action='store_true', default=False,
+                         help='Clears working directory of contents. Use of this flag is not'
+                              'recommended when running concurrent processes of fMRIPrep.')
+    g_other.add_argument(
+        '--resource-monitor', action='store_true', default=False,
+        help='enable Nipype\'s resource monitoring to keep track of memory and CPU usage')
+    g_other.add_argument(
+        '--reports-only', action='store_true', default=False,
+        help='only generate reports, don\'t run workflows. This will only rerun report '
+             'aggregation, not reportlet generation for specific nodes.')
+    g_other.add_argument(
+        '--run-uuid', action='store', default=None,
+        help='Specify UUID of previous run, to include error logs in report. '
+             'No effect without --reports-only.')
+    g_other.add_argument('--write-graph', action='store_true', default=False,
+                         help='Write workflow graph.')
+    g_other.add_argument('--stop-on-first-crash', action='store_true', default=False,
+                         help='Force stopping on first crash, even if a work directory'
+                              ' was specified.')
+    g_other.add_argument('--notrack', action='store_true', default=False,
+                         help='Opt-out of sending tracking information of this run to '
+                              'the FMRIPREP developers. This information helps to '
+                              'improve FMRIPREP and provides an indicator of real '
+                              'world usage crucial for obtaining funding.')
+    g_other.add_argument('--sloppy', action='store_true', default=False,
+                         help='Use low-quality tools for speed - TESTING ONLY')
+
+    latest = check_latest()
+    if latest is not None and currentv < latest:
+        parser.warning("""\
+You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.
+Please check out our documentation about how and when to upgrade:
+https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (
+            config.execution.version, latest))
+
+    _blist = is_flagged()
+    if _blist[0]:
+        _reason = _blist[1] or 'unknown'
+        parser.warning("""\
+WARNING: Version %s of fMRIPrep (current) has been FLAGGED
+(reason: %s).
+That means some severe flaw was found in it and we strongly
+discourage its usage.""" % (config.execution.version, _reason))
+
+    return parser
+
+
+def parse_args(args=None, namespace=None):
+    """Parse args and run further checks on the command line."""
+    import logging
+    parser = _build_parser()
+    opts = parser.parse_args(args, namespace)
+    config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
+    config.from_dict(vars(opts))
+
+    config.set_logger_level()
+
+    # Retrieve logging level
+    build_log = config.loggers.cli
+
+    if config.execution.fs_license_file is None:
+        raise RuntimeError("""\
+ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing \
+license file at several paths, in this order: 1) command line argument ``--fs-license-file``; \
+2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \
+(for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html""")
+    os.environ['FS_LICENSE'] = config.execution.fs_license_file
+
+    # Load base plugin_settings from file if --use-plugin
+    if opts.use_plugin is not None:
+        from yaml import load as loadyml
+        with open(opts.use_plugin) as f:
+            plugin_settings = loadyml(f)
+        _plugin = plugin_settings.get('plugin')
+        if _plugin:
+            config.nipype.plugin = _plugin
+            config.nipype.plugin_args = plugin_settings.get('plugin_args', {})
+            config.nipype.nprocs = config.nipype.plugin_args.get('nprocs', config.nipype.nprocs)
+
+    # Resource management options
+    # Note that we're making strong assumptions about valid plugin args
+    # This may need to be revisited if people try to use batch plugins
+    if 1 < config.nipype.nprocs < config.nipype.omp_nthreads:
+        build_log.warning(
+            'Per-process threads (--omp-nthreads=%d) exceed total '
+            'threads (--nthreads/--n_cpus=%d)', config.nipype.omp_nthread, config.nipype.nprocs)
+
+    bids_dir = config.execution.bids_dir
+    output_dir = config.execution.output_dir
+    work_dir = config.execution.work_dir
+    version = config.execution.version
+
+    if config.execution.fs_subjects_dir is None:
+        config.execution.fs_subjects_dir = output_dir / 'freesurfer'
+
+    # Wipe out existing work_dir
+    if opts.clean_workdir and work_dir.exists():
+        from niworkflows.utils.misc import clean_directory
+        build_log.log("Clearing previous fMRIPrep working directory: %s",
+                      work_dir)
+        if not clean_directory(work_dir):
+            build_log.warning("Could not clear all contents of working directory: %s",
+                              work_dir)
+
+    # Ensure input and output folders are not the same
+    if output_dir == bids_dir:
+        parser.error(
+            'The selected output folder is the same as the input BIDS folder. '
+            'Please modify the output path (suggestion: %s).'
+            % bids_dir / 'derivatives' / ('fmriprep-%s' % version.split('+')[0])
+        )
+
+    if bids_dir in work_dir.parents:
+        parser.error(
+            'The selected working directory is a subdirectory of the input BIDS folder. '
+            'Please modify the output path.'
+        )
+
+    # Validate inputs
+    if not opts.skip_bids_validation:
+        from ..utils.bids import validate_input_dir
+        build_log.info(
+            "Making sure the input data is BIDS compliant (warnings can be ignored in most "
+            "cases)."
+        )
+        validate_input_dir(config.execution.exec_env, opts.bids_dir, opts.participant_label)
+
+    # Setup directories
+    config.execution.log_dir = output_dir / 'fmriprep' / 'logs'
+    # Check and create output and working directories
+    config.execution.log_dir.mkdir(exist_ok=True, parents=True)
+    output_dir.mkdir(exist_ok=True, parents=True)
+    work_dir.mkdir(exist_ok=True, parents=True)
+
+    # First check that bids_dir looks like a BIDS folder
+    config.init_layout()
+    participant_label = set(config.execution.participant_label)
+    missing_subjects = participant_label - set(config.execution.layout.get_subjects())
+    if missing_subjects:
+        parser.error(
+            "One or more participant labels were not found in the BIDS directory: "
+            "%s." % ", ".join(missing_subjects))
+
+    config.execution.participant_label = sorted(participant_label)
+    config.workflow.skull_strip_template = config.workflow.skull_strip_template[0]
+
+    # Ensure user-defined spatial references for outputs are correctly parsed.
+    # Certain options require normalization to a space not explicitly defined by users.
+    # These spaces will not be included in the final outputs.
+    internal_spaces = []
+    if config.workflow.use_aroma:
+        # Make sure there's a normalization to FSL for AROMA to use.
+        internal_spaces.append('MNI152NLin6Asym:res-2')
+
+    cifti_output = config.workflow.cifti_output
+    if cifti_output:
+        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
+        vol_res = '2' if cifti_output == '91k' else '1'
+        internal_spaces += ['fsaverage:den-164k', 'MNI152NLin6Asym:res-%s' % vol_res]
+
+    # These arguments implicitly signal expected output
+    spaces = config.execution.output_spaces
+    # Add the default standard space if not already present (required by several sub-workflows)
+    if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
+        internal_spaces.append("MNI152NLin2009cAsym")
+
+    config.workflow.internal_spaces = ' '.join(internal_spaces) or None
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index 7339a5117..cdb3ca29c 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -1,392 +1,103 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 """fMRI preprocessing workflow."""
-
-import os
-import re
-from pathlib import Path
-import logging
-import sys
-import gc
-import uuid
-import warnings
-import json
-from argparse import ArgumentParser
-from argparse import ArgumentDefaultsHelpFormatter
-from multiprocessing import cpu_count
-from time import strftime
-
-logging.addLevelName(25, 'IMPORTANT')  # Add a new level between INFO and WARNING
-logging.addLevelName(15, 'VERBOSE')  # Add a new level between INFO and DEBUG
-logger = logging.getLogger('cli')
-
-
-def _warn_redirect(message, category, filename, lineno, file=None, line=None):
-    logger.warning('Captured warning (%s): %s', category, message)
-
-
-def check_deps(workflow):
-    from nipype.utils.filemanip import which
-    return sorted(
-        (node.interface.__class__.__name__, node.interface._cmd)
-        for node in workflow._get_all_nodes()
-        if (hasattr(node.interface, '_cmd') and
-            which(node.interface._cmd.split()[0]) is None))
-
-
-def get_parser():
-    """Build parser object."""
-    from packaging.version import Version
-    from ..__about__ import __version__
-    from .version import check_latest, is_flagged
-    from niworkflows.utils.spaces import Reference, SpatialReferences, OutputReferencesAction
-
-    verstr = 'fMRIPrep v{}'.format(__version__)
-    currentv = Version(__version__)
-    is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
-
-    parser = ArgumentParser(description='fMRIPrep: fMRI PREProcessing workflows',
-                            formatter_class=ArgumentDefaultsHelpFormatter)
-
-    # Arguments as specified by BIDS-Apps
-    # required, positional arguments
-    # IMPORTANT: they must go directly with the parser object
-    parser.add_argument('bids_dir', action='store', type=Path,
-                        help='the root folder of a BIDS valid dataset (sub-XXXXX folders should '
-                             'be found at the top level in this folder).')
-    parser.add_argument('output_dir', action='store', type=Path,
-                        help='the output path for the outcomes of preprocessing and visual '
-                             'reports')
-    parser.add_argument('analysis_level', choices=['participant'],
-                        help='processing stage to be run, only "participant" in the case of '
-                             'fMRIPrep (see BIDS-Apps specification).')
-
-    # optional arguments
-    parser.add_argument('--version', action='version', version=verstr)
-
-    g_bids = parser.add_argument_group('Options for filtering BIDS queries')
-    g_bids.add_argument('--skip_bids_validation', '--skip-bids-validation', action='store_true',
-                        default=False,
-                        help='assume the input dataset is BIDS compliant and skip the validation')
-    g_bids.add_argument('--participant_label', '--participant-label', action='store', nargs='+',
-                        help='a space delimited list of participant identifiers or a single '
-                             'identifier (the sub- prefix can be removed)')
-    # Re-enable when option is actually implemented
-    # g_bids.add_argument('-s', '--session-id', action='store', default='single_session',
-    #                     help='select a specific session to be processed')
-    # Re-enable when option is actually implemented
-    # g_bids.add_argument('-r', '--run-id', action='store', default='single_run',
-    #                     help='select a specific run to be processed')
-    g_bids.add_argument(
-        '--bids-filter-file', action='store', type=Path, metavar='PATH',
-        help='a JSON file describing custom BIDS input filter using pybids '
-             '{<suffix>:{<entity>:<filter>,...},...} '
-             '(https://github.com/bids-standard/pybids/blob/master/bids/layout/config/bids.json)')
-    g_bids.add_argument('-t', '--task-id', action='store',
-                        help='select a specific task to be processed')
-    g_bids.add_argument('--echo-idx', action='store', type=int,
-                        help='select a specific echo to be processed in a multiecho series')
-
-    g_perfm = parser.add_argument_group('Options to handle performance')
-    g_perfm.add_argument('--nthreads', '--n_cpus', '-n-cpus', action='store', type=int,
-                         help='maximum number of threads across all processes')
-    g_perfm.add_argument('--omp-nthreads', action='store', type=int, default=0,
-                         help='maximum number of threads per-process')
-    g_perfm.add_argument('--mem_mb', '--mem-mb', action='store', default=0, type=int,
-                         help='upper bound memory limit for FMRIPREP processes')
-    g_perfm.add_argument('--low-mem', action='store_true',
-                         help='attempt to reduce memory usage (will increase disk usage '
-                              'in working directory)')
-    g_perfm.add_argument('--use-plugin', action='store', default=None,
-                         help='nipype plugin configuration file')
-    g_perfm.add_argument('--anat-only', action='store_true',
-                         help='run anatomical workflows only')
-    g_perfm.add_argument('--boilerplate', action='store_true',
-                         help='generate boilerplate only')
-    g_perfm.add_argument('--md-only-boilerplate', action='store_true',
-                         default=False,
-                         help='skip generation of HTML and LaTeX formatted citation with pandoc')
-    g_perfm.add_argument('--error-on-aroma-warnings', action='store_true',
-                         default=False,
-                         help='Raise an error if ICA_AROMA does not produce sensible output '
-                              '(e.g., if all the components are classified as signal or noise)')
-    g_perfm.add_argument("-v", "--verbose", dest="verbose_count", action="count", default=0,
-                         help="increases log verbosity for each occurence, debug level is -vvv")
-
-    g_conf = parser.add_argument_group('Workflow configuration')
-    g_conf.add_argument(
-        '--ignore', required=False, action='store', nargs="+", default=[],
-        choices=['fieldmaps', 'slicetiming', 'sbref', 't2w', 'flair'],
-        help='ignore selected aspects of the input dataset to disable corresponding '
-             'parts of the workflow (a space delimited list)')
-    g_conf.add_argument(
-        '--longitudinal', action='store_true',
-        help='treat dataset as longitudinal - may increase runtime')
-    g_conf.add_argument(
-        '--t2s-coreg', action='store_true',
-        help='If provided with multi-echo BOLD dataset, create T2*-map and perform '
-             'T2*-driven coregistration. When multi-echo data is provided and this '
-             'option is not enabled, standard EPI-T1 coregistration is performed '
-             'using the middle echo.')
-    g_conf.add_argument(
-        '--output-spaces', nargs='*', action=OutputReferencesAction, default=SpatialReferences(),
-        help="""\
-Standard and non-standard spaces to resample anatomical and functional images to. \
-Standard spaces may be specified by the form \
-``<SPACE>[:cohort-<label>][:res-<resolution>][...]``, where ``<SPACE>`` is \
-a keyword designating a spatial reference, and may be followed by optional, \
-colon-separated parameters. \
-Non-standard spaces imply specific orientations and sampling grids. \
-Important to note, the ``res-*`` modifier does not define the resolution used for \
-the spatial normalization. To generate no BOLD outputs, use this option without specifying \
-any spatial references. For further details, please check out \
-https://fmriprep.readthedocs.io/en/%s/spaces.html""" % (currentv.base_version
-                                                        if is_release else 'latest'))
-
-    g_conf.add_argument('--bold2t1w-dof', action='store', default=6, choices=[6, 9, 12], type=int,
-                        help='Degrees of freedom when registering BOLD to T1w images. '
-                             '6 degrees (rotation and translation) are used by default.')
-    g_conf.add_argument(
-        '--force-bbr', action='store_true', dest='use_bbr', default=None,
-        help='Always use boundary-based registration (no goodness-of-fit checks)')
-    g_conf.add_argument(
-        '--force-no-bbr', action='store_false', dest='use_bbr', default=None,
-        help='Do not use boundary-based registration (no goodness-of-fit checks)')
-    g_conf.add_argument(
-        '--medial-surface-nan', required=False, action='store_true', default=False,
-        help='Replace medial wall values with NaNs on functional GIFTI files. Only '
-        'performed for GIFTI files mapped to a freesurfer subject (fsaverage or fsnative).')
-    g_conf.add_argument(
-        '--dummy-scans', required=False, action='store', default=None, type=int,
-        help='Number of non steady state volumes.')
-
-    # ICA_AROMA options
-    g_aroma = parser.add_argument_group('Specific options for running ICA_AROMA')
-    g_aroma.add_argument('--use-aroma', action='store_true', default=False,
-                         help='add ICA_AROMA to your preprocessing stream')
-    g_aroma.add_argument('--aroma-melodic-dimensionality', action='store',
-                         default=-200, type=int,
-                         help='Exact or maximum number of MELODIC components to estimate '
-                         '(positive = exact, negative = maximum)')
-
-    # Confounds options
-    g_confounds = parser.add_argument_group('Specific options for estimating confounds')
-    g_confounds.add_argument(
-        '--return-all-components', required=False, action='store_true', default=False,
-        help='Include all components estimated in CompCor decomposition in the confounds '
-             'file instead of only the components sufficient to explain 50 percent of '
-             'BOLD variance in each CompCor mask')
-    g_confounds.add_argument(
-        '--fd-spike-threshold', required=False, action='store', default=0.5, type=float,
-        help='Threshold for flagging a frame as an outlier on the basis of framewise '
-             'displacement')
-    g_confounds.add_argument(
-        '--dvars-spike-threshold', required=False, action='store', default=1.5, type=float,
-        help='Threshold for flagging a frame as an outlier on the basis of standardised '
-             'DVARS')
-
-    #  ANTs options
-    g_ants = parser.add_argument_group('Specific options for ANTs registrations')
-    g_ants.add_argument(
-        '--skull-strip-template', default='OASIS30ANTs', type=Reference.from_string,
-        help='select a template for skull-stripping with antsBrainExtraction')
-    g_ants.add_argument('--skull-strip-fixed-seed', action='store_true',
-                        help='do not use a random seed for skull-stripping - will ensure '
-                             'run-to-run replicability when used with --omp-nthreads 1')
-
-    # Fieldmap options
-    g_fmap = parser.add_argument_group('Specific options for handling fieldmaps')
-    g_fmap.add_argument('--fmap-bspline', action='store_true', default=False,
-                        help='fit a B-Spline field using least-squares (experimental)')
-    g_fmap.add_argument('--fmap-no-demean', action='store_false', default=True,
-                        help='do not remove median (within mask) from fieldmap')
-
-    # SyN-unwarp options
-    g_syn = parser.add_argument_group('Specific options for SyN distortion correction')
-    g_syn.add_argument('--use-syn-sdc', action='store_true', default=False,
-                       help='EXPERIMENTAL: Use fieldmap-free distortion correction')
-    g_syn.add_argument('--force-syn', action='store_true', default=False,
-                       help='EXPERIMENTAL/TEMPORARY: Use SyN correction in addition to '
-                       'fieldmap correction, if available')
-
-    # FreeSurfer options
-    g_fs = parser.add_argument_group('Specific options for FreeSurfer preprocessing')
-    g_fs.add_argument(
-        '--fs-license-file', metavar='PATH', type=Path,
-        help='Path to FreeSurfer license key file. Get it (for free) by registering'
-             ' at https://surfer.nmr.mgh.harvard.edu/registration.html')
-    g_fs.add_argument(
-        '--fs-subjects-dir', metavar='PATH', type=Path,
-        help='Path to existing FreeSurfer subjects directory to reuse. '
-             '(default: OUTPUT_DIR/freesurfer)')
-
-    # Surface generation xor
-    g_surfs = parser.add_argument_group('Surface preprocessing options')
-    g_surfs.add_argument('--no-submm-recon', action='store_false', dest='hires',
-                         help='disable sub-millimeter (hires) reconstruction')
-    g_surfs_xor = g_surfs.add_mutually_exclusive_group()
-    g_surfs_xor.add_argument('--cifti-output', nargs='?', const='91k', default=False,
-                             choices=('91k', '170k'), type=str,
-                             help='output preprocessed BOLD as a CIFTI dense timeseries. '
-                             'Optionally, the number of grayordinate can be specified '
-                             '(default is 91k, which equates to 2mm resolution)')
-    g_surfs_xor.add_argument('--fs-no-reconall',
-                             action='store_false', dest='run_reconall',
-                             help='disable FreeSurfer surface preprocessing.')
-
-    g_other = parser.add_argument_group('Other options')
-    g_other.add_argument('-w', '--work-dir', action='store', type=Path, default=Path('work'),
-                         help='path where intermediate results should be stored')
-    g_other.add_argument('--clean-workdir', action='store_true', default=False,
-                         help='Clears working directory of contents. Use of this flag is not'
-                              'recommended when running concurrent processes of fMRIPrep.')
-    g_other.add_argument(
-        '--resource-monitor', action='store_true', default=False,
-        help='enable Nipype\'s resource monitoring to keep track of memory and CPU usage')
-    g_other.add_argument(
-        '--reports-only', action='store_true', default=False,
-        help='only generate reports, don\'t run workflows. This will only rerun report '
-             'aggregation, not reportlet generation for specific nodes.')
-    g_other.add_argument(
-        '--run-uuid', action='store', default=None,
-        help='Specify UUID of previous run, to include error logs in report. '
-             'No effect without --reports-only.')
-    g_other.add_argument('--write-graph', action='store_true', default=False,
-                         help='Write workflow graph.')
-    g_other.add_argument('--stop-on-first-crash', action='store_true', default=False,
-                         help='Force stopping on first crash, even if a work directory'
-                              ' was specified.')
-    g_other.add_argument('--notrack', action='store_true', default=False,
-                         help='Opt-out of sending tracking information of this run to '
-                              'the FMRIPREP developers. This information helps to '
-                              'improve FMRIPREP and provides an indicator of real '
-                              'world usage crucial for obtaining funding.')
-    g_other.add_argument('--sloppy', action='store_true', default=False,
-                         help='Use low-quality tools for speed - TESTING ONLY')
-
-    latest = check_latest()
-    if latest is not None and currentv < latest:
-        print("""\
-You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.
-Please check out our documentation about how and when to upgrade:
-https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (
-            __version__, latest), file=sys.stderr)
-
-    _blist = is_flagged()
-    if _blist[0]:
-        _reason = _blist[1] or 'unknown'
-        print("""\
-WARNING: Version %s of fMRIPrep (current) has been FLAGGED
-(reason: %s).
-That means some severe flaw was found in it and we strongly
-discourage its usage.""" % (__version__, _reason), file=sys.stderr)
-
-    return parser
+from .. import config
 
 
 def main():
-    """Entry point"""
-    from nipype import logging as nlogging
-    from multiprocessing import set_start_method, Process, Manager
-    from ..utils.bids import write_derivative_description, validate_input_dir
-    set_start_method('forkserver')
-    warnings.showwarning = _warn_redirect
-    opts = get_parser().parse_args()
-
-    exec_env = os.name
+    """Entry point."""
+    import os
+    import sys
+    import gc
+    from nipype import config as ncfg
+    from multiprocessing import Process, Manager
+    from .parser import parse_args
+    from ..utils.bids import write_derivative_description
 
-    # special variable set in the container
-    if os.getenv('IS_DOCKER_8395080871'):
-        exec_env = 'singularity'
-        cgroup = Path('/proc/1/cgroup')
-        if cgroup.exists() and 'docker' in cgroup.read_text():
-            exec_env = 'docker'
-            if os.getenv('DOCKER_VERSION_8395080871'):
-                exec_env = 'fmriprep-docker'
+    parse_args()
 
     sentry_sdk = None
-    if not opts.notrack:
+    if not config.execution.notrack:
         import sentry_sdk
         from ..utils.sentry import sentry_setup
-        sentry_setup(opts, exec_env)
+        sentry_setup()
 
-    # Validate inputs
-    if not opts.skip_bids_validation:
-        print("Making sure the input data is BIDS compliant (warnings can be ignored in most "
-              "cases).")
-        validate_input_dir(exec_env, opts.bids_dir, opts.participant_label)
+    config_file = config.execution.work_dir / '.fmriprep.toml'
+    config.to_filename(config_file)
 
-    # FreeSurfer license
-    default_license = str(Path(os.getenv('FREESURFER_HOME')) / 'license.txt')
-    # Precedence: --fs-license-file, $FS_LICENSE, default_license
-    license_file = opts.fs_license_file or Path(os.getenv('FS_LICENSE', default_license))
-    if not license_file.exists():
-        raise RuntimeError("""\
-ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing \
-license file at several paths, in this order: 1) command line argument ``--fs-license-file``; \
-2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \
-(for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html""")
-    os.environ['FS_LICENSE'] = str(license_file.resolve())
-
-    # Retrieve logging level
-    log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
-    # Set logging
-    logger.setLevel(log_level)
-    logger.addHandler(logging.StreamHandler())
-    nlogging.getLogger('nipype.workflow').setLevel(log_level)
-    nlogging.getLogger('nipype.interface').setLevel(log_level)
-    nlogging.getLogger('nipype.utils').setLevel(log_level)
-
-    # Call build_workflow(opts, retval)
+    # 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=(opts, retval))
+        p = Process(target=build_workflow, args=(str(config_file), retval))
         p.start()
         p.join()
 
         retcode = p.exitcode or retval.get('return_code', 0)
-
-        bids_dir = Path(retval.get('bids_dir'))
-        output_dir = Path(retval.get('output_dir'))
-        work_dir = Path(retval.get('work_dir'))
-        plugin_settings = retval.get('plugin_settings', None)
-        subject_list = retval.get('subject_list', None)
         fmriprep_wf = retval.get('workflow', None)
-        run_uuid = retval.get('run_uuid', None)
 
-    if opts.reports_only:
-        sys.exit(int(retcode > 0))
+    config.load(config_file)
 
-    if opts.boilerplate:
+    if config.execution.reports_only:
         sys.exit(int(retcode > 0))
 
-    if fmriprep_wf and opts.write_graph:
+    if fmriprep_wf and config.execution.write_graph:
         fmriprep_wf.write_graph(graph2use="colored", format='svg', simple_form=True)
 
-    retcode = retcode or int(fmriprep_wf is None)
+    retcode = retcode or (fmriprep_wf is None) * os.EX_SOFTWARE
     if retcode != 0:
         sys.exit(retcode)
 
-    # Check workflow for missing commands
-    missing = check_deps(fmriprep_wf)
-    if missing:
-        print("Cannot run fMRIPrep. Missing dependencies:", file=sys.stderr)
-        for iface, cmd in missing:
-            print("\t{} (Interface: {})".format(cmd, iface))
-        sys.exit(2)
+    # Generate boilerplate
+    with Manager() as mgr:
+        from .workflow import build_boilerplate
+        p = Process(target=build_boilerplate,
+                    args=(str(config_file), fmriprep_wf))
+        p.start()
+        p.join()
+
+    if config.execution.boilerplate_only:
+        sys.exit(int(retcode > 0))
+
     # Clean up master process before running workflow, which may create forks
     gc.collect()
 
-    # Sentry tracking
-    if not opts.notrack:
-        from ..utils.sentry import start_ping
-        start_ping(run_uuid, len(subject_list))
+    # Nipype config (logs and execution)
+    ncfg.update_config({
+        'logging': {
+            'log_directory': str(config.execution.log_dir),
+            'log_to_file': True
+        },
+        'execution': {
+            'crashdump_dir': str(config.execution.log_dir),
+            'crashfile_format': 'txt',
+            'get_linked_libs': False,
+            'stop_on_first_crash': config.nipype.stop_on_first_crash,
+        },
+        'monitoring': {
+            'enabled': config.nipype.resource_monitor,
+            'sample_frequency': '0.5',
+            'summary_append': True,
+        }
+    })
 
+    if config.nipype.resource_monitor:
+        ncfg.enable_resource_monitor()
+
+    # Sentry tracking
+    if sentry_sdk is not None:
+        with sentry_sdk.configure_scope() as scope:
+            scope.set_tag('run_uuid', config.execution.run_uuid)
+            scope.set_tag('npart', len(config.execution.participant_label))
+        sentry_sdk.add_breadcrumb(message='fMRIPrep started', level='info')
+        sentry_sdk.capture_message('fMRIPrep started', level='info')
+
+    config.loggers.workflow.log(25, 'fMRIPrep started!')
     errno = 1  # Default is error exit unless otherwise set
     try:
-        fmriprep_wf.run(**plugin_settings)
+        fmriprep_wf.run(**config.nipype.get_plugin())
     except Exception as e:
-        if not opts.notrack:
+        if not config.execution.notrack:
             from ..utils.sentry import process_crashfile
             crashfolders = [output_dir / 'fmriprep' / 'sub-{}'.format(s) / 'log' / run_uuid
                             for s in subject_list]
@@ -396,10 +107,17 @@ def main():
 
             if "Workflow did not execute cleanly" not in str(e):
                 sentry_sdk.capture_exception(e)
-        logger.critical('fMRIPrep failed: %s', e)
+        config.loggers.workflow.critical('fMRIPrep failed: %s', e)
         raise
     else:
-        if opts.run_reconall:
+
+        config.loggers.workflow.log(25, 'fMRIPrep finished successfully!')
+        if not config.execution.notrack:
+            success_message = 'fMRIPrep finished without errors'
+            sentry_sdk.add_breadcrumb(message=success_message, level='info')
+            sentry_sdk.capture_message(success_message, level='info')
+
+        if config.workflow.run_reconall:
             from templateflow import api
             from niworkflows.utils.misc import _copy_any
             dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
@@ -408,10 +126,6 @@ def main():
             _copy_any(dseg_tsv,
                       str(output_dir / 'fmriprep' / 'desc-aparcaseg_dseg.tsv'))
         errno = 0
-        logger.log(25, 'fMRIPrep finished without errors')
-        if not opts.notrack:
-            sentry_sdk.capture_message('fMRIPrep finished without errors',
-                                       level='info')
     finally:
         from niworkflows.reports import generate_reports
         from subprocess import check_call, CalledProcessError, TimeoutExpired
@@ -423,7 +137,7 @@ def main():
             for ext in ('bib', 'tex', 'md', 'html')
         }
 
-        if not opts.md_only_boilerplate and citation_files['md'].exists():
+        if not config.execution.md_only_boilerplate and citation_files['md'].exists():
             # Generate HTML file resolving citations
             cmd = ['pandoc', '-s', '--bibliography',
                    pkgrf('fmriprep', 'data/boilerplate.bib'),
@@ -432,31 +146,34 @@ def main():
                    str(citation_files['md']),
                    '-o', str(citation_files['html'])]
 
-            logger.info('Generating an HTML version of the citation boilerplate...')
+            config.loggers.cli.info(
+                'Generating an HTML version of the citation boilerplate...')
             try:
                 check_call(cmd, timeout=10)
             except (FileNotFoundError, CalledProcessError, TimeoutExpired):
-                logger.warning('Could not generate CITATION.html file:\n%s',
-                               ' '.join(cmd))
+                config.loggers.cli.warning(
+                    'Could not generate CITATION.html file:\n%s', ' '.join(cmd))
 
             # Generate LaTex file resolving citations
             cmd = ['pandoc', '-s', '--bibliography',
                    pkgrf('fmriprep', 'data/boilerplate.bib'),
                    '--natbib', str(citation_files['md']),
                    '-o', str(citation_files['tex'])]
-            logger.info('Generating a LaTeX version of the citation boilerplate...')
+            config.loggers.cli.info(
+                'Generating a LaTeX version of the citation boilerplate...')
             try:
                 check_call(cmd, timeout=10)
             except (FileNotFoundError, CalledProcessError, TimeoutExpired):
-                logger.warning('Could not generate CITATION.tex file:\n%s',
-                               ' '.join(cmd))
+                config.loggers.cli.warning(
+                    'Could not generate CITATION.tex file:\n%s', ' '.join(cmd))
             else:
                 copyfile(pkgrf('fmriprep', 'data/boilerplate.bib'),
                          citation_files['bib'])
         else:
-            logger.warning('fMRIPrep could not find the markdown version of '
-                           'the citation boilerplate (%s). HTML and LaTeX versions'
-                           ' of it will not be available', citation_files['md'])
+            config.loggers.cli.warning(
+                'fMRIPrep could not find the markdown version of '
+                'the citation boilerplate (%s). HTML and LaTeX versions'
+                ' of it will not be available', citation_files['md'])
 
         # Generate reports phase
         failed_reports = generate_reports(
@@ -465,281 +182,13 @@ def main():
             packagename='fmriprep')
         write_derivative_description(bids_dir, output_dir / 'fmriprep')
 
-        if failed_reports and not opts.notrack:
+        if failed_reports and not config.execution.notrack:
             sentry_sdk.capture_message(
                 'Report generation failed for %d subjects' % failed_reports,
                 level='error')
         sys.exit(int((errno + failed_reports) > 0))
 
 
-def build_workflow(opts, retval):
-    """
-    Create the Nipype Workflow that supports the whole execution
-    graph, given the inputs.
-
-    All the checks and the construction of the workflow are done
-    inside this function that has pickleable inputs and output
-    dictionary (``retval``) to allow isolation using a
-    ``multiprocessing.Process`` that allows fmriprep to enforce
-    a hard-limited memory-scope.
-
-    """
-    from bids import BIDSLayout
-
-    from nipype import logging as nlogging, config as ncfg
-    from niworkflows.utils.bids import collect_participants, check_pipeline_version
-    from niworkflows.reports import generate_reports
-    from ..__about__ import __version__
-    from ..workflows.base import init_fmriprep_wf
-
-    build_log = nlogging.getLogger('nipype.workflow')
-
-    INIT_MSG = """
-    Running fMRIPREP version {version}:
-      * BIDS dataset path: {bids_dir}.
-      * Participant list: {subject_list}.
-      * Run identifier: {uuid}.
-
-    {spaces}
-    """.format
-
-    bids_dir = opts.bids_dir.resolve()
-    output_dir = opts.output_dir.resolve()
-    work_dir = opts.work_dir.resolve()
-    bids_filters = json.loads(opts.bids_filter_file.read_text()) if opts.bids_filter_file else None
-
-    if opts.clean_workdir:
-        from niworkflows.utils.misc import clean_directory
-        build_log.info("Clearing previous fMRIPrep working directory: %s" % work_dir)
-        if not clean_directory(work_dir):
-            build_log.warning("Could not clear all contents of working directory: %s" % work_dir)
-
-    retval['return_code'] = 1
-    retval['workflow'] = None
-    retval['bids_dir'] = str(bids_dir)
-    retval['output_dir'] = str(output_dir)
-    retval['work_dir'] = str(work_dir)
-
-    if output_dir == bids_dir:
-        build_log.error(
-            'The selected output folder is the same as the input BIDS folder. '
-            'Please modify the output path (suggestion: %s).',
-            bids_dir / 'derivatives' / ('fmriprep-%s' % __version__.split('+')[0]))
-        retval['return_code'] = 1
-        return retval
-
-    # warn if older results exist
-    msg = check_pipeline_version(
-        __version__, output_dir / 'fmriprep' / 'dataset_description.json'
-    )
-    if msg is not None:
-        build_log.warning(msg)
-
-    if bids_dir in work_dir.parents:
-        build_log.error(
-            'The selected working directory is a subdirectory of the input BIDS folder. '
-            'Please modify the output path.')
-        retval['return_code'] = 1
-        return retval
-
-    # Set up some instrumental utilities
-    run_uuid = '%s_%s' % (strftime('%Y%m%d-%H%M%S'), uuid.uuid4())
-    retval['run_uuid'] = run_uuid
-
-    # First check that bids_dir looks like a BIDS folder
-    layout = BIDSLayout(str(bids_dir), validate=False,
-                        ignore=("code", "stimuli", "sourcedata", "models",
-                                "derivatives", re.compile(r'^\.')))
-    subject_list = collect_participants(
-        layout, participant_label=opts.participant_label)
-    retval['subject_list'] = subject_list
-
-    # Load base plugin_settings from file if --use-plugin
-    if opts.use_plugin is not None:
-        from yaml import load as loadyml
-        with open(opts.use_plugin) as f:
-            plugin_settings = loadyml(f)
-        plugin_settings.setdefault('plugin_args', {})
-    else:
-        # Defaults
-        plugin_settings = {
-            'plugin': 'MultiProc',
-            'plugin_args': {
-                'raise_insufficient': False,
-                'maxtasksperchild': 1,
-            }
-        }
-
-    # Resource management options
-    # Note that we're making strong assumptions about valid plugin args
-    # This may need to be revisited if people try to use batch plugins
-    nthreads = plugin_settings['plugin_args'].get('n_procs')
-    # Permit overriding plugin config with specific CLI options
-    if nthreads is None or opts.nthreads is not None:
-        nthreads = opts.nthreads
-        if nthreads is None or nthreads < 1:
-            nthreads = cpu_count()
-        plugin_settings['plugin_args']['n_procs'] = nthreads
-
-    if opts.mem_mb:
-        plugin_settings['plugin_args']['memory_gb'] = opts.mem_mb / 1024
-
-    omp_nthreads = opts.omp_nthreads
-    if omp_nthreads == 0:
-        omp_nthreads = min(nthreads - 1 if nthreads > 1 else cpu_count(), 8)
-
-    if 1 < nthreads < omp_nthreads:
-        build_log.warning(
-            'Per-process threads (--omp-nthreads=%d) exceed total '
-            'threads (--nthreads/--n_cpus=%d)', omp_nthreads, nthreads)
-    retval['plugin_settings'] = plugin_settings
-
-    # Set up directories
-    log_dir = output_dir / 'fmriprep' / 'logs'
-    # Check and create output and working directories
-    output_dir.mkdir(exist_ok=True, parents=True)
-    log_dir.mkdir(exist_ok=True, parents=True)
-    work_dir.mkdir(exist_ok=True, parents=True)
-
-    # Nipype config (logs and execution)
-    ncfg.update_config({
-        'logging': {
-            'log_directory': str(log_dir),
-            'log_to_file': True
-        },
-        'execution': {
-            'crashdump_dir': str(log_dir),
-            'crashfile_format': 'txt',
-            'get_linked_libs': False,
-            'stop_on_first_crash': opts.stop_on_first_crash,
-        },
-        'monitoring': {
-            'enabled': opts.resource_monitor,
-            'sample_frequency': '0.5',
-            'summary_append': True,
-        }
-    })
-
-    if opts.resource_monitor:
-        ncfg.enable_resource_monitor()
-
-    # Called with reports only
-    if opts.reports_only:
-        from pkg_resources import resource_filename as pkgrf
-
-        build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
-        if opts.run_uuid is not None:
-            run_uuid = opts.run_uuid
-            retval['run_uuid'] = run_uuid
-        retval['return_code'] = generate_reports(
-            subject_list, output_dir, work_dir, run_uuid,
-            config=pkgrf('fmriprep', 'data/reports-spec.yml'),
-            packagename='fmriprep')
-        return retval
-
-    # Build main workflow
-    build_log.log(25, INIT_MSG(
-        version=__version__,
-        bids_dir=bids_dir,
-        subject_list=subject_list,
-        uuid=run_uuid,
-        spaces=opts.output_spaces)
-    )
-
-    retval['workflow'] = init_fmriprep_wf(
-        anat_only=opts.anat_only,
-        aroma_melodic_dim=opts.aroma_melodic_dimensionality,
-        bold2t1w_dof=opts.bold2t1w_dof,
-        cifti_output=opts.cifti_output,
-        debug=opts.sloppy,
-        dummy_scans=opts.dummy_scans,
-        echo_idx=opts.echo_idx,
-        err_on_aroma_warn=opts.error_on_aroma_warnings,
-        fmap_bspline=opts.fmap_bspline,
-        fmap_demean=opts.fmap_no_demean,
-        force_syn=opts.force_syn,
-        freesurfer=opts.run_reconall,
-        fs_subjects_dir=opts.fs_subjects_dir,
-        hires=opts.hires,
-        ignore=opts.ignore,
-        layout=layout,
-        longitudinal=opts.longitudinal,
-        low_mem=opts.low_mem,
-        medial_surface_nan=opts.medial_surface_nan,
-        omp_nthreads=omp_nthreads,
-        output_dir=str(output_dir),
-        run_uuid=run_uuid,
-        regressors_all_comps=opts.return_all_components,
-        regressors_fd_th=opts.fd_spike_threshold,
-        regressors_dvars_th=opts.dvars_spike_threshold,
-        skull_strip_fixed_seed=opts.skull_strip_fixed_seed,
-        skull_strip_template=opts.skull_strip_template[0],
-        spaces=parse_spaces(opts),
-        subject_list=subject_list,
-        t2s_coreg=opts.t2s_coreg,
-        task_id=opts.task_id,
-        use_aroma=opts.use_aroma,
-        use_bbr=opts.use_bbr,
-        use_syn=opts.use_syn_sdc,
-        work_dir=str(work_dir),
-        bids_filters=bids_filters,
-    )
-    retval['return_code'] = 0
-
-    logs_path = Path(output_dir) / 'fmriprep' / 'logs'
-    boilerplate = retval['workflow'].visit_desc()
-
-    if boilerplate:
-        citation_files = {
-            ext: logs_path / ('CITATION.%s' % ext)
-            for ext in ('bib', 'tex', 'md', 'html')
-        }
-        # To please git-annex users and also to guarantee consistency
-        # among different renderings of the same file, first remove any
-        # existing one
-        for citation_file in citation_files.values():
-            try:
-                citation_file.unlink()
-            except FileNotFoundError:
-                pass
-
-        citation_files['md'].write_text(boilerplate)
-        build_log.log(25, 'Works derived from this fMRIPrep execution should '
-                      'include the following boilerplate:\n\n%s', boilerplate)
-    return retval
-
-
-def parse_spaces(opts):
-    """
-    Ensure user-defined spatial references for outputs are correctly parsed.
-
-    Certain options require normalization to a space not explicitly defined by users.
-    These spaces will not be included in the final outputs.
-
-    """
-    spaces = opts.output_spaces
-    if not spaces.references and not spaces.is_cached():
-        spaces.add('MNI152NLin2009cAsym')
-
-    if not spaces.is_cached():  # spaces may be already checkpointed if users want no BOLD outputs
-        spaces.checkpoint()
-
-    if opts.use_aroma:
-        # Make sure there's a normalization to FSL for AROMA to use.
-        spaces.add(('MNI152NLin6Asym', {'res': '2'}))
-
-    if opts.cifti_output:
-        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
-        vol_res = '2' if opts.cifti_output == '91k' else '1'
-        spaces.add(('fsaverage', {'den': '164k'}))
-        spaces.add(('MNI152NLin6Asym', {'res': vol_res}))
-
-    # Add the default standard space if not already present (required by several sub-workflows)
-    if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        spaces.add("MNI152NLin2009cAsym")
-    return spaces
-
-
 if __name__ == '__main__':
     raise RuntimeError("fmriprep/cli/run.py should not be run directly;\n"
                        "Please `pip install` fmriprep and use the `fmriprep` command")
diff --git a/fmriprep/cli/tests/test_parser.py b/fmriprep/cli/tests/test_parser.py
new file mode 100644
index 000000000..1781a725f
--- /dev/null
+++ b/fmriprep/cli/tests/test_parser.py
@@ -0,0 +1,68 @@
+"""Test parser."""
+import pytest
+from ..parser import _build_parser
+
+MIN_ARGS = ['data/', 'out/', 'participant']
+
+
+@pytest.mark.parametrize('args,code', [
+    ([], 2),
+    (MIN_ARGS, 2),  # bids_dir does not exist
+    (MIN_ARGS + ['--fs-license-file'], 2),
+    (MIN_ARGS + ['--fs-license-file', 'fslicense.txt'], 2),
+])
+def test_parser_errors(args, code):
+    """Check behavior of the parser."""
+    with pytest.raises(SystemExit) as error:
+        _build_parser().parse_args(args)
+
+    assert error.value.code == code
+
+
+@pytest.mark.parametrize('args', [
+    MIN_ARGS,
+    MIN_ARGS + ['--fs-license-file'],
+])
+def test_parser_valid(tmp_path, args):
+    """Check valid arguments."""
+    datapath = (tmp_path / 'data')
+    datapath.mkdir(exist_ok=True)
+    args[0] = str(datapath)
+
+    if '--fs-license-file' in args:
+        _fs_file = tmp_path / 'license.txt'
+        _fs_file.write_text('')
+        args.insert(args.index('--fs-license-file') + 1,
+                    str(_fs_file.absolute()))
+
+    opts = _build_parser().parse_args(args)
+
+    assert opts.bids_dir == datapath
+
+
+@pytest.mark.parametrize('argval,gb', [
+    ('1G', 1),
+    ('1GB', 1),
+    ('1000', 1),    # Default units are MB
+    ('32000', 32),  # Default units are MB
+    ('4000', 4),    # Default units are MB
+    ('1000M', 1),
+    ('1000MB', 1),
+    ('1T', 1000),
+    ('1TB', 1000),
+    ('%dK' % 1e6, 1),
+    ('%dKB' % 1e6, 1),
+    ('%dB' % 1e9, 1),
+])
+def test_memory_arg(tmp_path, argval, gb):
+    """Check the correct parsing of the memory argument."""
+    datapath = (tmp_path / 'data')
+    datapath.mkdir(exist_ok=True)
+    _fs_file = tmp_path / 'license.txt'
+    _fs_file.write_text('')
+
+    args = MIN_ARGS + ['--fs-license-file', str(_fs_file)] \
+        + ['--mem', argval]
+    opts = _build_parser().parse_args(args)
+
+    assert opts.memory_gb == gb
diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
new file mode 100644
index 000000000..b3ccccf09
--- /dev/null
+++ b/fmriprep/cli/workflow.py
@@ -0,0 +1,122 @@
+"""
+The workflow builder factory method.
+
+All the checks and the construction of the workflow are done
+inside this function that has pickleable inputs and output
+dictionary (``retval``) to allow isolation using a
+``multiprocessing.Process`` that allows fmriprep to enforce
+a hard-limited memory-scope.
+
+"""
+
+
+def build_workflow(config_file, retval):
+    """Create the Nipype Workflow that supports the whole execution graph."""
+    from niworkflows.utils.bids import collect_participants, check_pipeline_version
+    from niworkflows.reports import generate_reports
+    from .. import config
+    from ..utils.misc import check_deps
+    from ..workflows.base import init_fmriprep_wf
+
+    config.load(config_file)
+    build_log = config.loggers.workflow
+
+    output_dir = config.execution.output_dir
+    version = config.execution.version
+
+    retval['return_code'] = 1
+    retval['workflow'] = None
+
+    # warn if older results exist
+    msg = check_pipeline_version(
+        version, output_dir / 'fmriprep' / 'dataset_description.json'
+    )
+    if msg is not None:
+        build_log.warning(msg)
+
+    # First check that bids_dir looks like a BIDS folder
+    config.init_layout()
+    subject_list = collect_participants(
+        config.execution.layout,
+        participant_label=config.execution.participant_label
+    )
+
+    # Called with reports only
+    if config.execution.reports_only:
+        from pkg_resources import resource_filename as pkgrf
+
+        build_log.log(25, 'Running --reports-only on participants %s', ', '.join(subject_list))
+        retval['return_code'] = generate_reports(
+            subject_list,
+            config.execution.output_dir,
+            config.execution.work_dir,
+            config.execution.run_uuid,
+            config=pkgrf('fmriprep', 'data/reports-spec.yml'),
+            packagename='fmriprep')
+        return retval
+
+    # Build main workflow
+    INIT_MSG = """
+    Running fMRIPREP version {version}:
+      * BIDS dataset path: {bids_dir}.
+      * Participant list: {subject_list}.
+      * Run identifier: {uuid}.
+      * Output spaces: {spaces}.
+    """.format
+    build_log.log(25, INIT_MSG(
+        version=config.execution.version,
+        bids_dir=config.execution.bids_dir,
+        subject_list=subject_list,
+        uuid=config.execution.run_uuid,
+        spaces=config.execution.output_spaces)
+    )
+
+    retval['workflow'] = init_fmriprep_wf()
+
+    # Check workflow for missing commands
+    missing = check_deps(retval['workflow'])
+    if missing:
+        build_log.critical(
+            "Cannot run fMRIPrep. Missing dependencies:%s",
+            '\n\t* %s'.join(["{} (Interface: {})".format(cmd, iface)
+                             for iface, cmd in missing])
+        )
+        retval['return_code'] = 127  # 127 == command not found.
+        return retval
+
+    config.to_filename(config_file)
+    build_log.info(
+        "fMRIPrep workflow graph with %d nodes built successfully.",
+        len(retval['workflow']._get_all_nodes())
+    )
+    retval['return_code'] = 0
+    return retval
+
+
+def build_boilerplate(config_file, workflow):
+    """Write boilerplate in an isolated process."""
+    from .. import config
+
+    config.load(config_file)
+    logs_path = config.execution.output_dir / 'fmriprep' / 'logs'
+    boilerplate = workflow.visit_desc()
+
+    if boilerplate:
+        citation_files = {
+            ext: logs_path / ('CITATION.%s' % ext)
+            for ext in ('bib', 'tex', 'md', 'html')
+        }
+        # To please git-annex users and also to guarantee consistency
+        # among different renderings of the same file, first remove any
+        # existing one
+        for citation_file in citation_files.values():
+            try:
+                citation_file.unlink()
+            except FileNotFoundError:
+                pass
+
+        citation_files['md'].write_text(boilerplate)
+        config.loggers.workflow.log(
+            25, 'Works derived from this fMRIPrep execution should '
+            'include the following boilerplate:\n\n%s', boilerplate
+        )
diff --git a/fmriprep/config.py b/fmriprep/config.py
index efd545ecc..fa1cdcc4e 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -1,5 +1,361 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""fMRIPrep settings."""
+"""*fMRIPrep* settings."""
+import os
+import sys
+import logging
+import warnings
+from multiprocessing import set_start_method
+
+
+def redirect_warnings(message, category, filename, lineno, file=None, line=None):
+    """Redirect other warnings."""
+    logger = logging.getLogger()
+    logger.debug('Captured warning (%s): %s', category, message)
+
+
+warnings.showwarning = redirect_warnings
+
+try:
+    set_start_method('forkserver')
+except RuntimeError:
+    pass  # context has been already set
+finally:
+    # Defer all custom import for after initializing the forkserver and
+    # redirecting warnings
+    from uuid import uuid4
+    from pathlib import Path
+    from time import strftime
+    from niworkflows.utils.spaces import SpatialReferences as _SRs, Reference as _Ref
+    from nipype import logging as nlogging, __version__ as _nipype_ver
+    from . import __version__
+
+logging.addLevelName(25, 'IMPORTANT')  # Add a new level between INFO and WARNING
+logging.addLevelName(15, 'VERBOSE')  # Add a new level between INFO and DEBUG
 
 DEFAULT_MEMORY_MIN_GB = 0.01
+
+_exec_env = os.name
+# special variable set in the container
+if os.getenv('IS_DOCKER_8395080871'):
+    _exec_env = 'singularity'
+    _cgroup = Path('/proc/1/cgroup')
+    if _cgroup.exists() and 'docker' in _cgroup.read_text():
+        _exec_env = 'docker'
+        if os.getenv('DOCKER_VERSION_8395080871'):
+            _exec_env = 'fmriprep-docker'
+    del _cgroup
+
+_fs_license = os.getenv('FS_LICENSE')
+if _fs_license is None and os.getenv('FREESURFER_HOME'):
+    _fs_license = os.path.join(os.getenv('FREESURFER_HOME'), 'license.txt')
+
+
+class _Config:
+    """An abstract class forbidding instantiation."""
+
+    _paths = tuple()
+
+    def __init__(self):
+        """Avert instantiation."""
+        raise RuntimeError('Configuration type is not instantiable.')
+
+    @classmethod
+    def load(cls, settings):
+        """Store settings from a dictionary."""
+        for k, v in settings.items():
+            if v is None:
+                continue
+            if k in cls._paths:
+                setattr(cls, k, Path(v).absolute())
+                continue
+            if hasattr(cls, k):
+                setattr(cls, k, v)
+
+    @classmethod
+    def get(cls):
+        """Return defined settings."""
+        out = {}
+        for k, v in cls.__dict__.items():
+            if k.startswith('_') or v is None:
+                continue
+            if callable(getattr(cls, k)):
+                continue
+            if k in cls._paths:
+                v = str(v)
+            if isinstance(v, _SRs):
+                v = ' '.join([str(s) for s in v.references]) or None
+            if isinstance(v, _Ref):
+                v = str(v) or None
+            out[k] = v
+        return out
+
+
+class nipype(_Config):
+    """Nipype configuration."""
+
+    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."""
+    memory_gb = None
+    """Estimation in GB of the RAM this workflow can allocate at any given time."""
+    nprocs = os.cpu_count()
+    """Number of processes (compute tasks) that can be run in parallel (multiprocessing only)."""
+    omp_nthreads = os.cpu_count()
+    """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."""
+    version = _nipype_ver
+    """Nipype's current version."""
+
+    @classmethod
+    def get_plugin(cls):
+        """Format a dictionary for Nipype consumption."""
+        out = {
+            'plugin': cls.plugin,
+            'plugin_args': cls.plugin_args,
+        }
+        if cls.plugin in ('MultiProc', 'LegacyMultiProc'):
+            out['plugin_args']['nprocs'] = cls.nprocs
+            out['plugin_args']['memory_gb'] = cls.memory_gb
+        return out
+
+
+class execution(_Config):
+    """Configure workflow-level settings."""
+
+    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 = None
+    """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
+    echo_idx = None
+    """Select a particular echo for multi-echo EPI datasets."""
+    exec_env = _exec_env
+    """A string representing the execution platform."""
+    fs_license_file = _fs_license
+    """An existing file containing a FreeSurfer license."""
+    fs_subjects_dir = None
+    """FreeSurfer's subjects directory."""
+    layout = None
+    """The path to the exported index of a py:class:`~bids.layout.BIDSLayout` object."""
+    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 *fMRIPrep* using Sentry.io."""
+    output_dir = None
+    """Folder where derivatives will be stored."""
+    output_spaces = None
+    """List of (non)standard spaces designated as spatial references for outputs."""
+    reports_only = False
+    """Only build the reports, based on the reportlets found in a cached working directory."""
+    run_uuid = '%s_%s' % (strftime('%Y%m%d-%H%M%S'), uuid4())
+    """Unique identifier of this particular run."""
+    participant_label = None
+    """List of participant identifiers that are to be preprocessed."""
+    task_id = None
+    """Select a particular task from all available in the dataset."""
+    version = __version__
+    """*fMRIPrep*'s version."""
+    work_dir = Path('work').absolute()
+    """Path to a working directory where intermediate results will be available."""
+    write_graph = False
+    """Write out the computational graph corresponding to the planned preprocessing."""
+
+    _layout = None
+
+    _paths = (
+        'bids_dir',
+        'fs_license_file',
+        'fs_subjects_dir',
+        'layout',
+        'log_dir',
+        'output_dir',
+        'work_dir',
+    )
+
+
+# These variables are not necessary anymore
+del _fs_license
+del _exec_env
+del _nipype_ver
+
+
+class workflow(_Config):
+    """Configure anatomical workflow."""
+
+    anat_only = False
+    """Execute the anatomical preprocessing only."""
+    aroma_err_on_warn = None
+    """Cast AROMA warnings to errors."""
+    aroma_melodic_dim = None
+    """Number of ICA components to be estimated by MELODIC
+    (positive = exact, negative = maximum)."""
+    bold2t1w_dof = None
+    """Degrees of freedom of the BOLD-to-T1w registration steps."""
+    cifti_output = None
+    """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
+    dummy_scans = None
+    """Set a number of initial scans to be considered nonsteady states."""
+    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 *fMRIPrep*."""
+    internal_spaces = None
+    """Standard and nonstandard spaces."""
+    longitudinal = False
+    """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
+    medial_surface_nan = None
+    """Fill medial surface with NaNs (not-a-number) when sampling."""
+    regressors_all_comps = None
+    regressors_dvars_th = None
+    regressors_fd_th = None
+    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
+    """Standard and nonstandard spaces."""
+    t2s_coreg = None
+    r"""Co-register echos before generating the T2\* reference of ME-EPI."""
+    use_aroma = None
+    """Run ICA-AROMA."""
+    use_bbr = None
+    """Run boundary-based registration for BOLD-to-T1w registration (default: ``True``)."""
+    use_syn = None
+    """Run *fieldmap-less* susceptibility-derived distortions estimation
+    in the absence of any alternatives."""
+
+
+class loggers(_Config):
+    """Configure loggers."""
+
+    default = logging.getLogger()
+    cli = logging.getLogger('cli')
+    workflow = nlogging.getLogger('nipype.workflow')
+    interface = nlogging.getLogger('nipype.interface')
+    utils = nlogging.getLogger('nipype.utils')
+
+
+def from_dict(settings):
+    """Read settings from a flat dictionary."""
+    nipype.load(settings)
+    execution.load(settings)
+    workflow.load(settings)
+    set_logger_level()
+
+
+def load(filename):
+    """Load settings from file."""
+    from toml import loads
+    filename = Path(filename)
+    settings = loads(filename.read_text())
+    for sectionname, configs in settings.items():
+        section = getattr(sys.modules[__name__], sectionname)
+        section.load(configs)
+    set_logger_level()
+    init_spaces()
+
+
+def get(flat=False):
+    """Get config as a dict."""
+    settings = {
+        'nipype': nipype.get(),
+        'execution': execution.get(),
+        'workflow': workflow.get(),
+    }
+    if not flat:
+        return settings
+
+    return {'.'.join((section, k)): v
+            for section, configs in settings.items()
+            for k, v in configs.items()}
+
+
+def dumps():
+    """Format config into toml."""
+    from toml import dumps
+    return dumps(get())
+
+
+def to_filename(filename):
+    """Write settings to file."""
+    filename = Path(filename)
+    filename.write_text(dumps())
+
+
+def init_layout():
+    """Init a new layout."""
+    if execution._layout is None:
+        import re
+        from bids.layout import BIDSLayout
+        work_dir = execution.work_dir / 'bids.db'
+        work_dir.mkdir(exist_ok=True, parents=True)
+        execution._layout = BIDSLayout(
+            str(execution.bids_dir),
+            validate=False,
+            database_path=str(work_dir),
+            ignore=("code", "stimuli", "sourcedata", "models",
+                    "derivatives", re.compile(r'^\.')))
+    execution.layout = execution._layout
+
+
+def set_logger_level():
+    """Set the current log level to all nipype loggers."""
+    loggers.default.setLevel(execution.log_level)
+    loggers.cli.setLevel(execution.log_level)
+    loggers.interface.setLevel(execution.log_level)
+    loggers.workflow.setLevel(execution.log_level)
+    loggers.utils.setLevel(execution.log_level)
+
+
+def init_spaces(checkpoint=True):
+    """Get a spatial references."""
+    from niworkflows.utils.spaces import Reference, SpatialReferences
+    if getattr(workflow, 'spaces'):
+        return
+
+    spaces = getattr(execution, 'output_spaces')
+    if spaces is not None and not isinstance(spaces, _SRs):
+        spaces = SpatialReferences(
+            [ref for s in execution.output_spaces.split(' ')
+             for ref in Reference.from_string(s)]
+        )
+    if spaces is None:
+        spaces = _SRs()
+
+    if checkpoint:
+        spaces.checkpoint()
+
+    internal = getattr(workflow, 'internal_spaces')
+    if internal is not None and internal.strip():
+        spaces += [ref for s in internal.split(' ')
+                   for ref in Reference.from_string(s)]
+    workflow.spaces = spaces
diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
index a52e032fa..212d48b8b 100644
--- a/fmriprep/utils/bids.py
+++ b/fmriprep/utils/bids.py
@@ -1,12 +1,6 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-Utilities to handle BIDS inputs
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-"""
+"""Utilities to handle BIDS inputs."""
 import os
 import sys
 import json
diff --git a/fmriprep/utils/meepi.py b/fmriprep/utils/meepi.py
index 8dbf81707..4e23230f5 100644
--- a/fmriprep/utils/meepi.py
+++ b/fmriprep/utils/meepi.py
@@ -1,12 +1,6 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-Multi-echo EPI utilities
-------------------------
-
-"""
+"""Multi-echo EPI utilities."""
 
 
 def combine_meepi_source(in_files):
diff --git a/fmriprep/utils/misc.py b/fmriprep/utils/misc.py
new file mode 100644
index 000000000..d69bf1f43
--- /dev/null
+++ b/fmriprep/utils/misc.py
@@ -0,0 +1,13 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+"""Miscellaneous utilities."""
+
+
+def check_deps(workflow):
+    """Make sure dependencies are present in this system."""
+    from nipype.utils.filemanip import which
+    return sorted(
+        (node.interface.__class__.__name__, node.interface._cmd)
+        for node in workflow._get_all_nodes()
+        if (hasattr(node.interface, '_cmd') and
+            which(node.interface._cmd.split()[0]) is None))
diff --git a/fmriprep/utils/sentry.py b/fmriprep/utils/sentry.py
index 0394154d3..c383afed8 100644
--- a/fmriprep/utils/sentry.py
+++ b/fmriprep/utils/sentry.py
@@ -7,6 +7,8 @@
 from niworkflows.utils.misc import read_crashfile
 import sentry_sdk
 
+from .. import config
+
 CHUNK_SIZE = 16384
 # Group common events with pre specified fingerprints
 KNOWN_ERRORS = {
@@ -40,27 +42,18 @@
 }
 
 
-def start_ping(run_uuid, npart):
-    with sentry_sdk.configure_scope() as scope:
-        if run_uuid:
-            scope.set_tag('run_uuid', run_uuid)
-        scope.set_tag('npart', npart)
-    sentry_sdk.add_breadcrumb(message='fMRIPrep started', level='info')
-    sentry_sdk.capture_message('fMRIPrep started', level='info')
-
-
-def sentry_setup(opts, exec_env):
+def sentry_setup():
     from os import cpu_count
     import psutil
     import hashlib
-    from ..__about__ import __version__
 
+    exec_env = config.execution.exec_env
     environment = "prod"
-    release = __version__
-    if not __version__:
+    release = config.execution.version
+    if not release:
         environment = "dev"
         release = "dev"
-    elif int(os.getenv('FMRIPREP_DEV', '0')) or ('+' in __version__):
+    elif int(os.getenv('FMRIPREP_DEV', '0')) or ('+' in release):
         environment = "dev"
 
     sentry_sdk.init("https://d5a16b0c38d84d1584dfc93b9fb1ade6@sentry.io/1137693",
@@ -73,7 +66,7 @@ def sentry_setup(opts, exec_env):
         if exec_env == 'fmriprep-docker':
             scope.set_tag('docker_version', os.getenv('DOCKER_VERSION_8395080871'))
 
-        dset_desc_path = opts.bids_dir / 'dataset_description.json'
+        dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
         if dset_desc_path.exists():
             desc_content = dset_desc_path.read_bytes()
             scope.set_tag('dset_desc_sha256', hashlib.sha256(desc_content).hexdigest())
@@ -104,7 +97,7 @@ def sentry_setup(opts, exec_env):
             scope.set_tag('overcommit_memory', 'n/a')
             scope.set_tag('overcommit_limit', 'n/a')
 
-        for k, v in vars(opts).items():
+        for k, v in config.get(flat=True).items():
             scope.set_tag(k, v)
 
 
diff --git a/fmriprep/utils/testing.py b/fmriprep/utils/testing.py
index ebb0e093b..1bff108df 100644
--- a/fmriprep/utils/testing.py
+++ b/fmriprep/utils/testing.py
@@ -1,5 +1,3 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 8550a4cee..102561ddc 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -13,7 +13,6 @@
 import os
 from copy import deepcopy
 
-from nipype import __version__ as nipype_ver
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
 from niworkflows.interfaces.nilearn import NILEARN_VERSION
@@ -23,52 +22,16 @@
     BIDSInfo, BIDSDataGrabber, BIDSFreeSurferDir
 )
 from niworkflows.utils.bids import collect_data
+from niworkflows.utils.spaces import Reference
 from niworkflows.utils.misc import fix_multi_T1w_source_name
 from smriprep.workflows.anatomical import init_anat_preproc_wf
 
+from .. import config
 from ..interfaces import SubjectSummary, AboutSummary, DerivativesDataSink
-from ..__about__ import __version__
 from .bold import init_func_preproc_wf
 
 
-def init_fmriprep_wf(
-    anat_only,
-    aroma_melodic_dim,
-    bold2t1w_dof,
-    cifti_output,
-    debug,
-    dummy_scans,
-    echo_idx,
-    err_on_aroma_warn,
-    fmap_bspline,
-    fmap_demean,
-    force_syn,
-    freesurfer,
-    fs_subjects_dir,
-    hires,
-    ignore,
-    layout,
-    longitudinal,
-    low_mem,
-    medial_surface_nan,
-    omp_nthreads,
-    output_dir,
-    regressors_all_comps,
-    regressors_dvars_th,
-    regressors_fd_th,
-    run_uuid,
-    skull_strip_fixed_seed,
-    skull_strip_template,
-    spaces,
-    subject_list,
-    t2s_coreg,
-    task_id,
-    use_aroma,
-    use_bbr,
-    use_syn,
-    work_dir,
-    bids_filters,
-):
+def init_fmriprep_wf():
     """
     Build *fMRIPrep*'s pipeline.
 
@@ -90,192 +53,30 @@ def init_fmriprep_wf(
             from niworkflows.utils.spaces import Reference, SpatialReferences
 
             os.environ['FREESURFER_HOME'] = os.getcwd()
-            wf = init_fmriprep_wf(
-                anat_only=False,
-                aroma_melodic_dim=-200,
-                bold2t1w_dof=9,
-                cifti_output=False,
-                debug=False,
-                dummy_scans=None,
-                echo_idx=None,
-                err_on_aroma_warn=False,
-                fmap_bspline=False,
-                fmap_demean=True,
-                force_syn=True,
-                freesurfer=True,
-                fs_subjects_dir=None,
-                hires=True,
-                ignore=[],
-                layout=BIDSLayout('.'),
-                longitudinal=False,
-                low_mem=False,
-                medial_surface_nan=False,
-                omp_nthreads=1,
-                output_dir='.',
-                regressors_all_comps=False,
-                regressors_dvars_th=1.5,
-                regressors_fd_th=0.5,
-                run_uuid='X',
-                skull_strip_fixed_seed=False,
-                skull_strip_template=Reference('OASIS30ANTs'),
-                spaces=SpatialReferences(
-                    spaces=['MNI152Lin',
-                            ('fsaverage', {'density': '10k'}),
-                            'T1w',
-                            'fsnative'],
-                    checkpoint=True),
-                subject_list=['fmripreptest'],
-                t2s_coreg=False,
-                task_id='',
-                use_aroma=False,
-                use_bbr=True,
-                use_syn=True,
-                work_dir='.',
-                bids_filters=None,
-            )
-
-
-    Parameters
-    ----------
-    anat_only : :obj:`bool`
-        Disable functional workflows
-    bold2t1w_dof : 6, 9 or 12
-        Degrees-of-freedom for BOLD-T1w registration
-    cifti_output : :obj:`bool`
-        Generate bold CIFTI file in output spaces
-    debug : :obj:`bool`
-        Enable debugging outputs
-    dummy_scans : :obj:`int` or None
-        Number of volumes to consider as non steady state
-    echo_idx : :obj:`int` or None
-        Index of echo to preprocess in multiecho BOLD series,
-        or ``None`` to preprocess all
-    err_on_aroma_warn : :obj:`bool`
-        Do not fail on ICA-AROMA errors
-    fmap_bspline : :obj:`bool`
-        **Experimental**: Fit B-Spline field using least-squares
-    fmap_demean : :obj:`bool`
-        Demean voxel-shift map during unwarp
-    force_syn : :obj:`bool`
-        **Temporary**: Always run SyN-based SDC
-    freesurfer : :obj:`bool`
-        Enable FreeSurfer surface reconstruction (may increase runtime)
-    hires : :obj:`bool`
-        Enable sub-millimeter preprocessing in FreeSurfer
-    ignore : :obj:`list`
-        Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
-    layout : :py:class:`~bids.layout.BIDSLayout`
-        BIDS dataset layout
-    longitudinal : :obj:`bool`
-        Treat multiple sessions as longitudinal (may increase runtime)
-        See sub-workflows for specific differences
-    low_mem : :obj:`bool`
-        Write uncompressed .nii files in some cases to reduce memory usage
-    medial_surface_nan : :obj:`bool`
-        Replace medial wall values with NaNs on functional GIFTI files
-    omp_nthreads : :obj:`int`
-        Maximum number of threads an individual process may use
-    output_dir : :obj:`str`
-        Directory in which to save derivatives
-    regressors_all_comps : :obj:`bool`
-        Return all CompCor component time series instead of the top fraction
-    regressors_dvars_th : :obj:`float`
-        Criterion for flagging DVARS outliers
-    regressors_fd_th : :obj:`float`
-        Criterion for flagging framewise displacement outliers
-    run_uuid : :obj:`str`
-        Unique identifier for execution instance
-    skull_strip_template : tuple
-        Name of target template for brain extraction with ANTs' ``antsBrainExtraction``,
-        and corresponding dictionary of output-space modifiers.
-    skull_strip_fixed_seed : :obj:`bool`
-        Do not use a random seed for skull-stripping - will ensure
-        run-to-run replicability when used with --omp-nthreads 1
-    spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
-        A container for storing, organizing, and parsing spatial normalizations. Composed of
-        :py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references.
-        Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs
-        (e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references
-        (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in
-        the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a
-        dictionary with template specifications (e.g., a specification of ``{'resolution': 2}``
-        would lead to resampling on a 2mm resolution of the space).
-    subject_list : :obj:`list`
-        List of subject labels
-    t2s_coreg : :obj:`bool`
-        For multi-echo EPI, use the calculated T2*-map for T2*-driven coregistration
-    task_id : :obj:`str` or None
-        Task ID of BOLD series to preprocess, or ``None`` to preprocess all
-    use_aroma : :obj:`bool`
-        Perform ICA-AROMA on MNI-resampled functional series
-    use_bbr : :obj:`bool` or None
-        Enable/disable boundary-based registration refinement.
-        If ``None``, test BBR result for distortion before accepting.
-    use_syn : :obj:`bool`
-        **Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
-        If fieldmaps are present and enabled, this is not run, by default.
-    work_dir : :obj:`str`
-        Directory in which to store workflow execution state and temporary files
-    bids_filters : :obj:`dict`
-        Provides finer specification of the pipeline input files using pybids entities filters.
-        A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
+            wf = init_fmriprep_wf()
 
     """
     fmriprep_wf = Workflow(name='fmriprep_wf')
-    fmriprep_wf.base_dir = work_dir
+    fmriprep_wf.base_dir = config.execution.work_dir
 
+    freesurfer = config.workflow.run_reconall
     if freesurfer:
         fsdir = pe.Node(
             BIDSFreeSurferDir(
-                derivatives=output_dir,
+                derivatives=config.execution.output_dir,
                 freesurfer_home=os.getenv('FREESURFER_HOME'),
-                spaces=spaces.get_fs_spaces()),
-            name='fsdir_run_' + run_uuid.replace('-', '_'), run_without_submitting=True)
-        if fs_subjects_dir is not None:
-            fsdir.inputs.subjects_dir = str(fs_subjects_dir.absolute())
-
-    reportlets_dir = os.path.join(work_dir, 'reportlets')
-    for subject_id in subject_list:
-        single_subject_wf = init_single_subject_wf(
-            anat_only=anat_only,
-            aroma_melodic_dim=aroma_melodic_dim,
-            bold2t1w_dof=bold2t1w_dof,
-            cifti_output=cifti_output,
-            debug=debug,
-            dummy_scans=dummy_scans,
-            echo_idx=echo_idx,
-            err_on_aroma_warn=err_on_aroma_warn,
-            fmap_bspline=fmap_bspline,
-            fmap_demean=fmap_demean,
-            force_syn=force_syn,
-            freesurfer=freesurfer,
-            hires=hires,
-            ignore=ignore,
-            layout=layout,
-            longitudinal=longitudinal,
-            low_mem=low_mem,
-            medial_surface_nan=medial_surface_nan,
-            name="single_subject_" + subject_id + "_wf",
-            omp_nthreads=omp_nthreads,
-            output_dir=output_dir,
-            regressors_all_comps=regressors_all_comps,
-            regressors_dvars_th=regressors_dvars_th,
-            regressors_fd_th=regressors_fd_th,
-            reportlets_dir=reportlets_dir,
-            skull_strip_fixed_seed=skull_strip_fixed_seed,
-            skull_strip_template=skull_strip_template,
-            spaces=spaces,
-            subject_id=subject_id,
-            t2s_coreg=t2s_coreg,
-            task_id=task_id,
-            use_aroma=use_aroma,
-            use_bbr=use_bbr,
-            use_syn=use_syn,
-            bids_filters=bids_filters,
-        )
-
-        single_subject_wf.config['execution']['crashdump_dir'] = (
-            os.path.join(output_dir, "fmriprep", "sub-" + subject_id, 'log', run_uuid)
+                spaces=config.workflow.spaces.get_fs_spaces()),
+            name='fsdir_run_%s' % config.execution.run_uuid.replace('-', '_'),
+            run_without_submitting=True)
+        if config.execution.fs_subjects_dir is not None:
+            fsdir.inputs.subjects_dir = str(config.execution.fs_subjects_dir.absolute())
+
+    for subject_id in config.execution.participant_label:
+        single_subject_wf = init_single_subject_wf(subject_id)
+
+        single_subject_wf.config['execution']['crashdump_dir'] = str(
+            config.execution.output_dir / "fmriprep" / "-".join(("sub", subject_id))
+            / "log" / config.execution.run_uuid
         )
         for node in single_subject_wf._get_all_nodes():
             node.config = deepcopy(single_subject_wf.config)
@@ -288,45 +89,9 @@ def init_fmriprep_wf(
     return fmriprep_wf
 
 
-def init_single_subject_wf(
-    anat_only,
-    aroma_melodic_dim,
-    bold2t1w_dof,
-    cifti_output,
-    debug,
-    dummy_scans,
-    echo_idx,
-    err_on_aroma_warn,
-    fmap_bspline,
-    fmap_demean,
-    force_syn,
-    freesurfer,
-    hires,
-    ignore,
-    layout,
-    longitudinal,
-    low_mem,
-    medial_surface_nan,
-    name,
-    omp_nthreads,
-    output_dir,
-    reportlets_dir,
-    regressors_all_comps,
-    regressors_dvars_th,
-    regressors_fd_th,
-    skull_strip_fixed_seed,
-    skull_strip_template,
-    spaces,
-    subject_id,
-    t2s_coreg,
-    task_id,
-    use_aroma,
-    use_bbr,
-    use_syn,
-    bids_filters,
-):
+def init_single_subject_wf(subject_id):
     """
-    This workflow organizes the preprocessing pipeline for a single subject.
+    Organize the preprocessing pipeline for a single subject.
 
     It collects and reports information about the subject, and prepares
     sub-workflows to perform anatomical and functional preprocessing.
@@ -345,136 +110,12 @@ def init_single_subject_wf(
             from fmriprep.workflows.base import init_single_subject_wf
 
             BIDSLayout = namedtuple('BIDSLayout', ['root'])
-            wf = init_single_subject_wf(
-                anat_only=False,
-                aroma_melodic_dim=-200,
-                bold2t1w_dof=9,
-                cifti_output=False,
-                debug=False,
-                dummy_scans=None,
-                echo_idx=None,
-                err_on_aroma_warn=False,
-                fmap_bspline=False,
-                fmap_demean=True,
-                force_syn=True,
-                freesurfer=True,
-                hires=True,
-                ignore=[],
-                layout=BIDSLayout('.'),
-                longitudinal=False,
-                low_mem=False,
-                medial_surface_nan=False,
-                name='single_subject_wf',
-                omp_nthreads=1,
-                output_dir='.',
-                reportlets_dir='.',
-                regressors_all_comps=False,
-                regressors_dvars_th=1.5,
-                regressors_fd_th=0.5,
-                skull_strip_fixed_seed=False,
-                skull_strip_template=Reference('OASIS30ANTs'),
-                spaces=SpatialReferences(
-                    spaces=['MNI152Lin',
-                            ('fsaverage', {'density': '10k'}),
-                            'T1w',
-                            'fsnative'],
-                    checkpoint=True),
-                subject_id='test',
-                t2s_coreg=False,
-                task_id='',
-                use_aroma=False,
-                use_bbr=True,
-                use_syn=True,
-                bids_filters=None,
-            )
+            wf = init_single_subject_wf('test')
 
     Parameters
     ----------
-    anat_only : :obj:`bool`
-        Disable functional workflows
-    aroma_melodic_dim : :obj:`int`
-        Maximum number of components identified by MELODIC within ICA-AROMA
-        (default is -200, i.e., no limitation).
-    bold2t1w_dof : 6, 9 or 12
-        Degrees-of-freedom for BOLD-T1w registration
-    cifti_output : :obj:`bool`
-        Generate bold CIFTI file in output spaces
-    debug : :obj:`bool`
-        Enable debugging outputs
-    dummy_scans : :obj:`int` or None
-        Number of volumes to consider as non steady state
-    echo_idx : :obj:`int` or None
-        Index of echo to preprocess in multiecho BOLD series,
-        or ``None`` to preprocess all
-    err_on_aroma_warn : :obj:`bool`
-        Do not fail on ICA-AROMA errors
-    fmap_bspline : :obj:`bool`
-        **Experimental**: Fit B-Spline field using least-squares
-    fmap_demean : :obj:`bool`
-        Demean voxel-shift map during unwarp
-    force_syn : :obj:`bool`
-        **Temporary**: Always run SyN-based SDC
-    freesurfer : :obj:`bool`
-        Enable FreeSurfer surface reconstruction (may increase runtime)
-    hires : :obj:`bool`
-        Enable sub-millimeter preprocessing in FreeSurfer
-    ignore : :obj:`list`
-        Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
-    layout : :py:class:`~bids.layout.BIDSLayout`
-        BIDS dataset layout
-    longitudinal : :obj:`bool`
-        Treat multiple sessions as longitudinal (may increase runtime)
-        See sub-workflows for specific differences
-    low_mem : :obj:`bool`
-        Write uncompressed .nii files in some cases to reduce memory usage
-    medial_surface_nan : :obj:`bool`
-        Replace medial wall values with NaNs on functional GIFTI files
-    name : :obj:`str`
-        Name of workflow
-    omp_nthreads : :obj:`int`
-        Maximum number of threads an individual process may use
-    output_dir : :obj:`str`
-        Directory in which to save derivatives
-    reportlets_dir : :obj:`str`
-        Directory in which to save reportlets
-    regressors_all_comps : :obj:`bool`
-        Return all CompCor component time series instead of the top fraction
-    regressors_dvars_th : :obj:`float`
-        Criterion for flagging DVARS outliers
-    regressors_fd_th : :obj:`float`
-        Criterion for flagging framewise displacement outliers
-    skull_strip_fixed_seed : :obj:`bool`
-        Do not use a random seed for skull-stripping - will ensure
-        run-to-run replicability when used with --omp-nthreads 1
-    skull_strip_template : tuple
-        Name of target template for brain extraction with ANTs' ``antsBrainExtraction``,
-        and corresponding dictionary of output-space modifiers.
     subject_id : :obj:`str`
-        List of subject labels
-    t2s_coreg : :obj:`bool`
-        For multi-echo EPI, use the calculated T2*-map for T2*-driven coregistration
-    spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
-        A container for storing, organizing, and parsing spatial normalizations. Composed of
-        :py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references.
-        Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs
-        (e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references
-        (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in
-        the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a
-        dictionary with template specifications (e.g., a specification of ``{'resolution': 2}``
-        would lead to resampling on a 2mm resolution of the space).
-    task_id : :obj:`str` or None
-        Task ID of BOLD series to preprocess, or ``None`` to preprocess all
-    use_aroma : :obj:`bool`
-        Perform ICA-AROMA on MNI-resampled functional series
-    use_bbr : :obj:`bool` or None
-        Enable/disable boundary-based registration refinement.
-        If ``None``, test BBR result for distortion before accepting.
-    use_syn : :obj:`bool`
-        **Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
-        If fieldmaps are present and enabled, this is not run, by default.
-    bids_filters : :obj:`dict`
-        Provides finer specification of the pipeline input files using pybids entities filters.
-        A dict with the following structure {<suffix>:{<entity>:<filter>,...},...}
+        Subject label for this single-subject workflow.
 
     Inputs
     ------
@@ -482,25 +123,28 @@ def init_single_subject_wf(
         FreeSurfer's ``$SUBJECTS_DIR``.
 
     """
-    if name in ('single_subject_wf', 'single_subject_fmripreptest_wf'):
-        # for documentation purposes
-        subject_data = {
-            't1w': ['/completely/made/up/path/sub-01_T1w.nii.gz'],
-            'bold': ['/completely/made/up/path/sub-01_task-nback_bold.nii.gz']
-        }
-    else:
-        subject_data = collect_data(layout, subject_id, task_id, echo_idx,
-                                    bids_filters=bids_filters)[0]
-        if 'flair' in ignore:
-            subject_data['flair'] = []
-        if 't2w' in ignore:
-            subject_data['t2w'] = []
-
+    name = "single_subject_%s_wf" % subject_id
+    subject_data = collect_data(
+        config.execution.layout,
+        subject_id,
+        config.execution.task_id,
+        config.execution.echo_idx,
+        bids_filters=config.execution.bids_filters)[0]
+
+    if 'flair' in config.workflow.ignore:
+        subject_data['flair'] = []
+    if 't2w' in config.workflow.ignore:
+        subject_data['t2w'] = []
+
+    anat_only = config.workflow.anat_only
     # Make sure we always go through these two checks
-    if not anat_only and subject_data['bold'] == []:
-        raise Exception("No BOLD images found for participant {} and task {}. "
-                        "All workflows require BOLD images.".format(
-                            subject_id, task_id if task_id else '<all>'))
+    if not anat_only and not subject_data['bold']:
+        task_id = config.execution.task_id
+        raise RuntimeError(
+            "No BOLD images found for participant {} and task {}. "
+            "All workflows require BOLD images.".format(
+                subject_id, task_id if task_id else '<all>')
+        )
 
     if not subject_data['t1w']:
         raise Exception("No T1w images found for participant {}. "
@@ -514,7 +158,8 @@ def init_single_subject_wf(
 which is based on *Nipype* {nipype_ver}
 (@nipype1; @nipype2; RRID:SCR_002502).
 
-""".format(fmriprep_ver=__version__, nipype_ver=nipype_ver)
+""".format(fmriprep_ver=config.execution.version,
+           nipype_ver=config.nipype.version)
     workflow.__postdesc__ = """
 
 Many internal operations of *fMRIPrep* use
@@ -538,6 +183,9 @@ def init_single_subject_wf(
 
 """.format(nilearn_ver=NILEARN_VERSION)
 
+    spaces = config.workflow.spaces
+    reportlets_dir = str(config.execution.work_dir / 'reportlets')
+
     inputnode = pe.Node(niu.IdentityInterface(fields=['subjects_dir']),
                         name='inputnode')
 
@@ -547,13 +195,13 @@ def init_single_subject_wf(
                       name='bidssrc')
 
     bids_info = pe.Node(BIDSInfo(
-        bids_dir=layout.root, bids_validate=False), name='bids_info')
+        bids_dir=config.execution.bids_dir, bids_validate=False), name='bids_info')
 
     summary = pe.Node(SubjectSummary(std_spaces=spaces.get_spaces(nonstandard=False),
                                      nstd_spaces=spaces.get_spaces(standard=False)),
                       name='summary', run_without_submitting=True)
 
-    about = pe.Node(AboutSummary(version=__version__,
+    about = pe.Node(AboutSummary(version=config.execution.version,
                                  command=' '.join(sys.argv)),
                     name='about', run_without_submitting=True)
 
@@ -569,19 +217,20 @@ def init_single_subject_wf(
 
     # Preprocessing of T1w (includes registration to MNI)
     anat_preproc_wf = init_anat_preproc_wf(
-        bids_root=layout.root,
-        debug=debug,
-        freesurfer=freesurfer,
-        hires=hires,
-        longitudinal=longitudinal,
+        bids_root=str(config.execution.bids_dir),
+        debug=config.execution.debug is True,
+        freesurfer=config.workflow.run_reconall,
+        hires=config.workflow.hires,
+        longitudinal=config.workflow.longitudinal,
         name="anat_preproc_wf",
         num_t1w=len(subject_data['t1w']),
-        omp_nthreads=omp_nthreads,
-        output_dir=output_dir,
+        omp_nthreads=config.nipype.omp_nthreads,
+        output_dir=str(config.execution.output_dir),
         reportlets_dir=reportlets_dir,
         spaces=spaces,
-        skull_strip_fixed_seed=skull_strip_fixed_seed,
-        skull_strip_template=skull_strip_template,
+        skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
+        skull_strip_template=Reference.from_string(
+            config.workflow.skull_strip_template)[0],
     )
 
     workflow.connect([
@@ -612,35 +261,7 @@ def init_single_subject_wf(
         return workflow
 
     for bold_file in subject_data['bold']:
-        func_preproc_wf = init_func_preproc_wf(
-            aroma_melodic_dim=aroma_melodic_dim,
-            bold2t1w_dof=bold2t1w_dof,
-            bold_file=bold_file,
-            cifti_output=cifti_output,
-            debug=debug,
-            dummy_scans=dummy_scans,
-            err_on_aroma_warn=err_on_aroma_warn,
-            fmap_bspline=fmap_bspline,
-            fmap_demean=fmap_demean,
-            force_syn=force_syn,
-            freesurfer=freesurfer,
-            ignore=ignore,
-            layout=layout,
-            low_mem=low_mem,
-            medial_surface_nan=medial_surface_nan,
-            num_bold=len(subject_data['bold']),
-            omp_nthreads=omp_nthreads,
-            output_dir=output_dir,
-            reportlets_dir=reportlets_dir,
-            regressors_all_comps=regressors_all_comps,
-            regressors_fd_th=regressors_fd_th,
-            regressors_dvars_th=regressors_dvars_th,
-            spaces=spaces,
-            t2s_coreg=t2s_coreg,
-            use_aroma=use_aroma,
-            use_bbr=use_bbr,
-            use_syn=use_syn,
-        )
+        func_preproc_wf = init_func_preproc_wf(bold_file)
 
         workflow.connect([
             (anat_preproc_wf, func_preproc_wf,
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index ea2d4f166..c2003a091 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -12,8 +12,6 @@
 import os
 
 import nibabel as nb
-from nipype import logging
-
 from nipype.interfaces.fsl import Split as FSLSplit
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
@@ -23,7 +21,7 @@
 from niworkflows.interfaces.utils import DictMerge
 from niworkflows.func.util import init_bold_reference_wf
 
-from ...config import DEFAULT_MEMORY_MIN_GB
+from ... import config
 from ...utils.meepi import combine_meepi_source
 
 from ...interfaces import DerivativesDataSink
@@ -43,38 +41,7 @@
 from .outputs import init_func_derivatives_wf
 
 
-LOGGER = logging.getLogger('nipype.workflow')
-
-
-def init_func_preproc_wf(
-    aroma_melodic_dim,
-    bold2t1w_dof,
-    bold_file,
-    cifti_output,
-    debug,
-    dummy_scans,
-    err_on_aroma_warn,
-    fmap_bspline,
-    fmap_demean,
-    force_syn,
-    freesurfer,
-    ignore,
-    low_mem,
-    medial_surface_nan,
-    omp_nthreads,
-    output_dir,
-    regressors_all_comps,
-    regressors_dvars_th,
-    regressors_fd_th,
-    reportlets_dir,
-    spaces,
-    t2s_coreg,
-    use_aroma,
-    use_bbr,
-    use_syn,
-    layout=None,
-    num_bold=1,
-):
+def init_func_preproc_wf(bold_file):
     """
     This workflow controls the functional preprocessing stages of *fMRIPrep*.
 
@@ -87,111 +54,12 @@ def init_func_preproc_wf(
             from niworkflows.utils.spaces import SpatialReferences
             from fmriprep.workflows.bold import init_func_preproc_wf
             BIDSLayout = namedtuple('BIDSLayout', ['root'])
-            wf = init_func_preproc_wf(
-                aroma_melodic_dim=-200,
-                bold2t1w_dof=9,
-                bold_file='/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
-                cifti_output=False,
-                debug=False,
-                dummy_scans=None,
-                err_on_aroma_warn=False,
-                fmap_bspline=True,
-                fmap_demean=True,
-                force_syn=True,
-                freesurfer=True,
-                ignore=[],
-                low_mem=False,
-                medial_surface_nan=False,
-                omp_nthreads=1,
-                output_dir='.',
-                regressors_all_comps=False,
-                regressors_dvars_th=1.5,
-                regressors_fd_th=0.5,
-                reportlets_dir='.',
-                spaces=SpatialReferences(
-                    spaces=['MNI152Lin',
-                            ('fsaverage', {'density': '10k'}),
-                            'T1w',
-                            'fsnative'],
-                    checkpoint=True),
-                t2s_coreg=False,
-                use_aroma=False,
-                use_bbr=True,
-                use_syn=True,
-                layout=BIDSLayout('.'),
-                num_bold=1,
-            )
+            wf = init_func_preproc_wf()
 
     Parameters
     ----------
-    aroma_melodic_dim : :obj:`int`
-        Maximum number of components identified by MELODIC within ICA-AROMA
-        (default is -200, ie. no limitation).
-    bold2t1w_dof : 6, 9 or 12
-        Degrees-of-freedom for BOLD-T1w registration
-    bold_file : :obj:`str`
+    bold_file
         BOLD series NIfTI file
-    cifti_output : :obj:`bool`
-        Generate bold CIFTI file in output spaces
-    debug : :obj:`bool`
-        Enable debugging outputs
-    dummy_scans : :obj:`int` or None
-        Number of volumes to consider as non steady state
-    err_on_aroma_warn : :obj:`bool`
-        Do not crash on ICA-AROMA errors
-    fmap_bspline : :obj:`bool`
-        **Experimental**: Fit B-Spline field using least-squares
-    fmap_demean : :obj:`bool`
-        Demean voxel-shift map during unwarp
-    force_syn : :obj:`bool`
-        **Temporary**: Always run SyN-based SDC
-    freesurfer : :obj:`bool`
-        Enable FreeSurfer functional registration (bbregister) and resampling
-        BOLD series to FreeSurfer surface meshes.
-    ignore : :obj:`list`
-        Preprocessing steps to skip (may include "slicetiming", "fieldmaps")
-    low_mem : :obj:`bool`
-        Write uncompressed .nii files in some cases to reduce memory usage
-    medial_surface_nan : :obj:`bool`
-        Replace medial wall values with NaNs on functional GIFTI files
-    omp_nthreads : :obj:`int`
-        Maximum number of threads an individual process may use
-    output_dir : :obj:`str`
-        Directory in which to save derivatives
-    regressors_all_comps : :obj:`bool`
-        Return all CompCor component time series instead of the top fraction
-    regressors_dvars_th : :obj:`float`
-        Criterion for flagging DVARS outliers
-    regressors_fd_th : :obj:`float`
-        Criterion for flagging framewise displacement outliers
-    reportlets_dir : :obj:`str`
-        Absolute path of a directory in which reportlets will be temporarily stored
-    spaces : :py:class:`~niworkflows.utils.spaces.SpatialReferences`
-        A container for storing, organizing, and parsing spatial normalizations. Composed of
-        :py:class:`~niworkflows.utils.spaces.Reference` objects representing spatial references.
-        Each ``Reference`` contains a space, which is a string of either TemplateFlow template IDs
-        (e.g., ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNIPediatricAsym``), nonstandard references
-        (e.g., ``T1w`` or ``anat``, ``sbref``, ``run``, etc.), or a custom template located in
-        the TemplateFlow root directory. Each ``Reference`` may also contain a spec, which is a
-        dictionary with template specifications (e.g., a specification of ``{'resolution': 2}``
-        would lead to resampling on a 2mm resolution of the space).
-    t2s_coreg : :obj:`bool`
-        For multiecho EPI, use the calculated T2*-map for T2*-driven coregistration
-    use_aroma : :obj:`bool`
-        Perform ICA-AROMA on MNI-resampled functional series
-    use_bbr : :obj:`bool` or None
-        Enable/disable boundary-based registration refinement.
-        If ``None``, test BBR result for distortion before accepting.
-        When using ``t2s_coreg``, BBR will be enabled by default unless
-        explicitly specified otherwise.
-    use_syn : :obj:`bool`
-        **Experimental**: Enable ANTs SyN-based susceptibility distortion correction (SDC).
-        If fieldmaps are present and enabled, this is not run, by default.
-    layout : :py:class:`~bids.layout.BIDSLayout`
-        BIDSLayout structure to enable metadata retrieval
-    num_bold : :obj:`int`
-        Total number of BOLD files that have been set for preprocessing
-        (default is 1)
 
     Inputs
     ------
@@ -292,14 +160,16 @@ def init_func_preproc_wf(
         bold_tlen, mem_gb = _create_mem_gb(ref_file)
 
     wf_name = _get_wf_name(ref_file)
-    LOGGER.log(25, ('Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
-                    'Memory resampled/largemem=%.2f/%.2f GB.'),
-               ref_file, mem_gb['filesize'], bold_tlen, mem_gb['resampled'], mem_gb['largemem'])
+    config.loggers.workflow.log(
+        25, ('Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
+             'Memory resampled/largemem=%.2f/%.2f GB.'),
+        ref_file, mem_gb['filesize'], bold_tlen, mem_gb['resampled'], mem_gb['largemem'])
 
     sbref_file = None
     # For doc building purposes
     if not hasattr(layout, 'parse_file_entities'):
-        LOGGER.log(25, 'No valid layout: building empty workflow.')
+        config.loggers.workflow.log(
+            25, 'No valid layout: building empty workflow.')
         metadata = {
             'RepetitionTime': 2.0,
             'SliceTiming': [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
@@ -327,21 +197,24 @@ def init_func_preproc_wf(
         files = layout.get(return_type='file', **entities)
         refbase = os.path.basename(ref_file)
         if 'sbref' in ignore:
-            LOGGER.info("Single-band reference files ignored.")
+            config.loggers.workflow.info("Single-band reference files ignored.")
         elif files and multiecho:
-            LOGGER.warning("Single-band reference found, but not supported in "
-                           "multi-echo workflows at this time. Ignoring.")
+            config.loggers.workflow.warning(
+                "Single-band reference found, but not supported in "
+                "multi-echo workflows at this time. Ignoring.")
         elif files:
             sbref_file = files[0]
             sbbase = os.path.basename(sbref_file)
             if len(files) > 1:
-                LOGGER.warning(
+                config.loggers.workflow.warning(
                     "Multiple single-band reference files found for {}; using "
                     "{}".format(refbase, sbbase))
             else:
-                LOGGER.log(25, "Using single-band reference file {}".format(sbbase))
+                config.loggers.workflow.log(
+                    25, "Using single-band reference file {}".format(sbbase))
         else:
-            LOGGER.log(25, "No single-band-reference found for {}".format(refbase))
+            config.loggers.workflow.log(
+                25, "No single-band-reference found for {}".format(refbase))
 
         metadata = layout.get_metadata(ref_file)
 
@@ -360,8 +233,9 @@ def init_func_preproc_wf(
 
     # Check if MEEPI for T2* coregistration target
     if t2s_coreg and not multiecho:
-        LOGGER.warning("No multiecho BOLD images found for T2* coregistration. "
-                       "Using standard EPI-T1 coregistration.")
+        config.loggers.workflow.warning(
+            "No multiecho BOLD images found for T2* coregistration. "
+            "Using standard EPI-T1 coregistration.")
         t2s_coreg = False
 
     # By default, force-bbr for t2s_coreg unless user specifies otherwise
@@ -422,7 +296,7 @@ def init_func_preproc_wf(
             registration_dof=bold2t1w_dof,
             pe_direction=metadata.get("PhaseEncodingDirection"),
             tr=metadata.get("RepetitionTime")),
-        name='summary', mem_gb=DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
+        name='summary', mem_gb=config.DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
     summary.inputs.dummy_scans = dummy_scans
 
     func_derivatives_wf = init_func_derivatives_wf(
@@ -920,11 +794,13 @@ def init_func_preproc_wf(
     # Freesurfer
     freesurfer_spaces = spaces.get_fs_spaces()
     if freesurfer and freesurfer_spaces:
-        LOGGER.log(25, 'Creating BOLD surface-sampling workflow.')
-        bold_surf_wf = init_bold_surf_wf(mem_gb=mem_gb['resampled'],
-                                         surface_spaces=freesurfer_spaces,
-                                         medial_surface_nan=medial_surface_nan,
-                                         name='bold_surf_wf')
+        config.loggers.workflow.log(
+            25, 'Creating BOLD surface-sampling workflow.')
+        bold_surf_wf = init_bold_surf_wf(
+            mem_gb=mem_gb['resampled'],
+            surface_spaces=freesurfer_spaces,
+            medial_surface_nan=medial_surface_nan,
+            name='bold_surf_wf')
         workflow.connect([
             (inputnode, bold_surf_wf, [
                 ('t1w_preproc', 'inputnode.t1w_preproc'),
@@ -966,13 +842,13 @@ def init_func_preproc_wf(
     ds_report_summary = pe.Node(
         DerivativesDataSink(desc='summary', keep_dtype=True),
         name='ds_report_summary', run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB)
+        mem_gb=config.DEFAULT_MEMORY_MIN_GB)
 
     ds_report_validation = pe.Node(
         DerivativesDataSink(base_directory=reportlets_dir,
                             desc='validation', keep_dtype=True),
         name='ds_report_validation', run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB)
+        mem_gb=config.DEFAULT_MEMORY_MIN_GB)
 
     workflow.connect([
         (summary, ds_report_summary, [('out_report', 'in_file')]),
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index de01e70e5..010c69aa4 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/fmriprep/workflows/bold/registration.py
@@ -17,7 +17,6 @@
 import pkg_resources as pkgr
 
 from nipype.pipeline import engine as pe
-from nipype import logging
 from nipype.interfaces import utility as niu, fsl, c3
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 # See https://github.com/poldracklab/fmriprep/issues/768
@@ -35,9 +34,10 @@
 
 from ...config import DEFAULT_MEMORY_MIN_GB
 from ...interfaces import DerivativesDataSink
+from ... import config
 
 
-LOGGER = logging.getLogger('nipype.workflow')
+LOGGER = config.loggers.workflow
 
 
 def init_bold_reg_wf(freesurfer, use_bbr, bold2t1w_dof, mem_gb, omp_nthreads,
diff --git a/fmriprep/workflows/bold/stc.py b/fmriprep/workflows/bold/stc.py
index 1a3b28341..4fc1fd79f 100644
--- a/fmriprep/workflows/bold/stc.py
+++ b/fmriprep/workflows/bold/stc.py
@@ -7,14 +7,14 @@
 .. autofunction:: init_bold_stc_wf
 
 """
-from nipype import logging
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu, afni
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.utils import CopyXForm
+from ... import config
 
 
-LOGGER = logging.getLogger('nipype.workflow')
+LOGGER = config.loggers.workflow
 
 
 def init_bold_stc_wf(metadata, name='bold_stc_wf'):
diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py
index acd8e23e5..b5c335a66 100644
--- a/fmriprep/workflows/bold/t2s.py
+++ b/fmriprep/workflows/bold/t2s.py
@@ -7,7 +7,6 @@
 .. autofunction:: init_bold_t2s_wf
 
 """
-from nipype import logging
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
 
@@ -15,8 +14,10 @@
 from niworkflows.func.util import init_skullstrip_bold_wf
 
 from ...interfaces import T2SMap
+from ... import config
 
-LOGGER = logging.getLogger('nipype.workflow')
+
+LOGGER = config.loggers.workflow
 
 
 # pylint: disable=R0914
diff --git a/setup.cfg b/setup.cfg
index 36c570162..0c60f0840 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -27,7 +27,7 @@ install_requires =
     numpy
     pandas
     psutil >= 5.4
-    pybids >= 0.9.4
+    pybids >= 0.10.0
     pyyaml
     sdcflows ~= 1.2.0
     smriprep ~= 0.5.2

From 85d49c719eedc7d9b41a58dbbb14f132f0a1c916 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 3 Mar 2020 10:26:13 -0800
Subject: [PATCH 02/43] enh: add documentation text

---
 fmriprep/config.py | 106 +++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 102 insertions(+), 4 deletions(-)

diff --git a/fmriprep/config.py b/fmriprep/config.py
index fa1cdcc4e..a7684a106 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -1,15 +1,107 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""*fMRIPrep* settings."""
-import os
-import sys
-import logging
+r"""
+*fMRIPrep* settings.
+
+This module implements the memory structures to keep a consistent, singleton config.
+
+Example
+-------
+>>> from fmriprep import config
+>>> config_file = config.execution.work_dir / '.fmriprep.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
+
+The module also has a :py:func:`to_filename` function to allow writting out
+the settings to hard disk in *ToML* format, which looks like::
+
+    [nipype]
+    crashfile_format = "txt"
+    get_linked_libs = false
+    nprocs = 8
+    omp_nthreads = 8
+    plugin = "MultiProc"
+    resource_monitor = false
+    stop_on_first_crash = false
+    version = "1.5.0-dev+gdffcb7815"
+
+    [execution]
+    bids_dir = "/data/openfmri/ds000005"
+    boilerplate_only = false
+    exec_env = "posix"
+    fs_license_file = "/opt/freesurfer/license.txt"
+    fs_subjects_dir = "/data/openfmri/ds000005/derivatives/freesurfer-6.0.1"
+    log_dir = "/data/openfmri/ds000005/derivatives/fmriprep/logs"
+    log_level = 15
+    low_mem = false
+    md_only_boilerplate = false
+    notrack = true
+    output_dir = "/data/openfmri/ds000005/derivatives"
+    reports_only = false
+    run_uuid = "20200302-174345_9ba9f304-82de-4538-8c3a-570c5f5d8f2f"
+    participant_label = [ "01",]
+    version = "20.0.1+13.g3ca42930.dirty"
+    work_dir = "/home/oesteban/tmp/fmriprep-ds005/fprep-work2"
+    write_graph = false
+
+    [workflow]
+    anat_only = false
+    aroma_err_on_warn = false
+    aroma_melodic_dim = -200
+    bold2t1w_dof = 6
+    cifti_output = false
+    fmap_bspline = false
+    force_syn = false
+    hires = true
+    ignore = []
+    internal_spaces = "MNI152NLin2009cAsym"
+    longitudinal = false
+    medial_surface_nan = false
+    run_reconall = true
+    skull_strip_fixed_seed = false
+    skull_strip_template = "OASIS30ANTs"
+    t2s_coreg = false
+    use_aroma = false
+
+    [nipype.plugin_args]
+    maxtasksperchild = 1
+    raise_insufficient = false
+
+This config file is used to pass the settings across processes,
+using the :py:func:`load` function.
+
+Other responsibilities of the config module:
+
+  * Switching Python's ``multiprocessing`` to *forkserver* mode.
+  * Set up new logger levels (25: IMPORTANT, and 15: VERBOSE).
+  * Set up a warnings filter as soon as possible.
+  * Initialize runtime descriptive settings (e.g., default FreeSurfer license,
+    execution environment, nipype and *fMRIPrep* versions, etc.).
+  * Automated I/O magic operations:
+
+    * :obj:`Path` \<-\> :obj:`str` \<-\> :obj:`Path`).
+    * :py:class:`~niworkflows.util.spaces.SpatialReferences` \<-\> :obj:`str` \<-\>
+      :py:class:`~niworkflows.util.spaces.SpatialReferences`
+    * :py:class:`~bids.layout.BIDSLayout` \<-\> :obj:`str` \<-\>
+      :py:class:`~bids.layout.BIDSLayout`
+
+"""
 import warnings
 from multiprocessing import set_start_method
 
 
 def redirect_warnings(message, category, filename, lineno, file=None, line=None):
     """Redirect other warnings."""
+    import logging
     logger = logging.getLogger()
     logger.debug('Captured warning (%s): %s', category, message)
 
@@ -23,6 +115,10 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
 finally:
     # Defer all custom import for after initializing the forkserver and
     # redirecting warnings
+    import os
+    import sys
+    import logging
+
     from uuid import uuid4
     from pathlib import Path
     from time import strftime
@@ -30,6 +126,7 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
     from nipype import logging as nlogging, __version__ as _nipype_ver
     from . import __version__
 
+
 logging.addLevelName(25, 'IMPORTANT')  # Add a new level between INFO and WARNING
 logging.addLevelName(15, 'VERBOSE')  # Add a new level between INFO and DEBUG
 
@@ -282,6 +379,7 @@ def load(filename):
         section.load(configs)
     set_logger_level()
     init_spaces()
+    init_layout()
 
 
 def get(flat=False):

From 74c9c7ee4ee7df3f6c3f61fd6bcd106e04f42158 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 11:46:21 -0800
Subject: [PATCH 03/43] enh: put together all warning handling

---
 fmriprep/__about__.py |  4 +---
 fmriprep/__init__.py  | 27 +++++++++------------------
 fmriprep/config.py    |  7 +++++++
 3 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/fmriprep/__about__.py b/fmriprep/__about__.py
index 6fc141e3a..cc43bf16a 100644
--- a/fmriprep/__about__.py
+++ b/fmriprep/__about__.py
@@ -1,8 +1,6 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-Base module variables
-"""
+"""Base module variables."""
 from ._version import get_versions
 __version__ = get_versions()['version']
 del get_versions
diff --git a/fmriprep/__init__.py b/fmriprep/__init__.py
index 044f5379c..0d1e70e40 100644
--- a/fmriprep/__init__.py
+++ b/fmriprep/__init__.py
@@ -1,26 +1,17 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""
-This pipeline is developed by the Poldrack lab at Stanford University
-(https://poldracklab.stanford.edu/) for use at
-the Center for Reproducible Neuroscience (http://reproducibility.stanford.edu/),
-as well as for open-source software distribution.
-"""
+"""Top-module metadata."""
 
-from .__about__ import (  # noqa
-    __version__,
+from .__about__ import (
     __copyright__,
     __credits__,
     __packagename__,
+    __version__,
 )
 
-import warnings
-
-# cmp is not used by fmriprep, so ignore nipype-generated warnings
-warnings.filterwarnings('ignore', r'cmp not installed')
-warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
-warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
-warnings.simplefilter('ignore', DeprecationWarning)
-warnings.simplefilter('ignore', ResourceWarning)
+__all__ = [
+    '__copyright__',
+    '__credits__',
+    '__packagename__',
+    '__version__',
+]
diff --git a/fmriprep/config.py b/fmriprep/config.py
index a7684a106..951a27ed2 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -106,8 +106,15 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
     logger.debug('Captured warning (%s): %s', category, message)
 
 
+# cmp is not used by fmriprep, so ignore nipype-generated warnings
+warnings.filterwarnings('ignore', r'cmp not installed')
+warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
+warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
+warnings.simplefilter('ignore', DeprecationWarning)
+warnings.simplefilter('ignore', ResourceWarning)
 warnings.showwarning = redirect_warnings
 
+
 try:
     set_start_method('forkserver')
 except RuntimeError:

From 80e0342eecd5011bdfbc62c50fc89bfdaa6bbce1 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 12:32:55 -0800
Subject: [PATCH 04/43] enh: adapt to new anatomical workflow API

---
 fmriprep/workflows/base.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 102561ddc..aaddbf974 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -222,15 +222,15 @@ def init_single_subject_wf(subject_id):
         freesurfer=config.workflow.run_reconall,
         hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
-        name="anat_preproc_wf",
-        num_t1w=len(subject_data['t1w']),
         omp_nthreads=config.nipype.omp_nthreads,
         output_dir=str(config.execution.output_dir),
         reportlets_dir=reportlets_dir,
-        spaces=spaces,
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
+        skull_strip_mode='force',
         skull_strip_template=Reference.from_string(
             config.workflow.skull_strip_template)[0],
+        spaces=spaces,
+        t1w=subject_data['t1w'],
     )
 
     workflow.connect([

From 911669b1eb92e9353202fcc5a644b24d9c9242c0 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 12:54:52 -0800
Subject: [PATCH 05/43] fix: porting arguments to config settings

---
 fmriprep/workflows/base.py      |  10 +++
 fmriprep/workflows/bold/base.py | 154 ++++++++++++++------------------
 2 files changed, 76 insertions(+), 88 deletions(-)

diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index aaddbf974..5584cb556 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -260,6 +260,16 @@ def init_single_subject_wf(subject_id):
     if anat_only:
         return workflow
 
+    # Append the functional section to the existing anatomical exerpt
+    # That way we do not need to stream down the number of bold datasets
+    anat_preproc_wf.__postdesc__ = (anat_preproc_wf.__postdesc__ or '') + """
+
+Functional data preprocessing
+
+: For each of the {num_bold} BOLD runs found per subject (across all
+tasks and sessions), the following preprocessing was performed.
+""".format(num_bold=len(subject_data['bold']))
+
     for bold_file in subject_data['bold']:
         func_preproc_wf = init_func_preproc_wf(bold_file)
 
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index c2003a091..7008145e0 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -152,6 +152,12 @@ def init_func_preproc_wf(bold_file):
     bold_tlen = 10
     multiecho = isinstance(bold_file, list)
 
+    # Have some options handy
+    layout = config.execution.layout
+    omp_nthreads = config.nipype.omp_nthreads
+    freesurfer = config.workflow.run_reconall
+    spaces = config.execution.output_spaces
+
     if multiecho:
         tes = [layout.get_metadata(echo)['EchoTime'] for echo in bold_file]
         ref_file = dict(zip(tes, bold_file))[min(tes)]
@@ -166,92 +172,62 @@ def init_func_preproc_wf(bold_file):
         ref_file, mem_gb['filesize'], bold_tlen, mem_gb['resampled'], mem_gb['largemem'])
 
     sbref_file = None
-    # For doc building purposes
-    if not hasattr(layout, 'parse_file_entities'):
-        config.loggers.workflow.log(
-            25, 'No valid layout: building empty workflow.')
-        metadata = {
-            'RepetitionTime': 2.0,
-            'SliceTiming': [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9],
-            'PhaseEncodingDirection': 'j',
-        }
-        fmaps = {
-            'phasediff': [{
-                'phases': [
-                    ('sub-03/ses-2/fmap/sub-03_ses-2_run-1_phasediff.nii.gz', {
-                        'EchoTime1': 0.0, 'EchoTime2': 0.00246
-                    })
-                ],
-                'magnitude': [
-                    ('sub-03/ses-2/fmap/sub-03_ses-2_run-1_magnitude1.nii.gz', {}),
-                    ('sub-03/ses-2/fmap/sub-03_ses-2_run-1_magnitude2.nii.gz', {})]
-            }]
-        }
-        run_stc = True
-        multiecho = False
-    else:
-        # Find associated sbref, if possible
-        entities = layout.parse_file_entities(ref_file)
-        entities['suffix'] = 'sbref'
-        entities['extension'] = ['nii', 'nii.gz']  # Overwrite extensions
-        files = layout.get(return_type='file', **entities)
-        refbase = os.path.basename(ref_file)
-        if 'sbref' in ignore:
-            config.loggers.workflow.info("Single-band reference files ignored.")
-        elif files and multiecho:
+    # Find associated sbref, if possible
+    entities = layout.parse_file_entities(ref_file)
+    entities['suffix'] = 'sbref'
+    entities['extension'] = ['nii', 'nii.gz']  # Overwrite extensions
+    files = layout.get(return_type='file', **entities)
+    refbase = os.path.basename(ref_file)
+    if 'sbref' in config.workflow.ignore:
+        config.loggers.workflow.info("Single-band reference files ignored.")
+    elif files and multiecho:
+        config.loggers.workflow.warning(
+            "Single-band reference found, but not supported in "
+            "multi-echo workflows at this time. Ignoring.")
+    elif files:
+        sbref_file = files[0]
+        sbbase = os.path.basename(sbref_file)
+        if len(files) > 1:
             config.loggers.workflow.warning(
-                "Single-band reference found, but not supported in "
-                "multi-echo workflows at this time. Ignoring.")
-        elif files:
-            sbref_file = files[0]
-            sbbase = os.path.basename(sbref_file)
-            if len(files) > 1:
-                config.loggers.workflow.warning(
-                    "Multiple single-band reference files found for {}; using "
-                    "{}".format(refbase, sbbase))
-            else:
-                config.loggers.workflow.log(
-                    25, "Using single-band reference file {}".format(sbbase))
+                "Multiple single-band reference files found for {}; using "
+                "{}".format(refbase, sbbase))
         else:
             config.loggers.workflow.log(
-                25, "No single-band-reference found for {}".format(refbase))
+                25, "Using single-band reference file {}".format(sbbase))
+    else:
+        config.loggers.workflow.log(
+            25, "No single-band-reference found for {}".format(refbase))
 
-        metadata = layout.get_metadata(ref_file)
+    metadata = layout.get_metadata(ref_file)
 
-        # Find fieldmaps. Options: (phase1|phase2|phasediff|epi|fieldmap|syn)
-        fmaps = None
-        if 'fieldmaps' not in ignore:
-            fmaps = fieldmap_wrangler(layout, ref_file, use_syn=use_syn, force_syn=force_syn)
-        elif use_syn or force_syn:
-            # If fieldmaps are not enabled, activate SyN-SDC in unforced (False) mode
-            fmaps = {'syn': False}
+    # Find fieldmaps. Options: (phase1|phase2|phasediff|epi|fieldmap|syn)
+    fmaps = None
+    if 'fieldmaps' not in config.workflow.ignore:
+        fmaps = fieldmap_wrangler(layout, ref_file,
+                                  use_syn=config.workflow.use_syn,
+                                  force_syn=config.workflow.force_syn)
+    elif config.workflow.use_syn or config.workflow.force_syn:
+        # If fieldmaps are not enabled, activate SyN-SDC in unforced (False) mode
+        fmaps = {'syn': False}
 
-        # Short circuits: (True and True and (False or 'TooShort')) == 'TooShort'
-        run_stc = (bool(metadata.get("SliceTiming")) and
-                   'slicetiming' not in ignore and
-                   (_get_series_len(ref_file) > 4 or "TooShort"))
+    # Short circuits: (True and True and (False or 'TooShort')) == 'TooShort'
+    run_stc = (bool(metadata.get("SliceTiming")) and
+               'slicetiming' not in config.workflow.ignore and
+               (_get_series_len(ref_file) > 4 or "TooShort"))
 
     # Check if MEEPI for T2* coregistration target
-    if t2s_coreg and not multiecho:
+    if config.workflow.t2s_coreg and not multiecho:
         config.loggers.workflow.warning(
             "No multiecho BOLD images found for T2* coregistration. "
             "Using standard EPI-T1 coregistration.")
         t2s_coreg = False
 
     # By default, force-bbr for t2s_coreg unless user specifies otherwise
-    if t2s_coreg and use_bbr is None:
+    if config.workflow.t2s_coreg and config.workflow.use_bbr is None:
         use_bbr = True
 
     # Build workflow
     workflow = Workflow(name=wf_name)
-    workflow.__desc__ = """
-
-Functional data preprocessing
-
-: For each of the {num_bold} BOLD runs found per subject (across all
-tasks and sessions), the following preprocessing was performed.
-""".format(num_bold=num_bold)
-
     workflow.__postdesc__ = """\
 All resamplings can be performed with *a single interpolation
 step* by composing all the pertinent transformations (i.e. head-motion
@@ -293,20 +269,20 @@ def init_func_preproc_wf(bold_file):
         FunctionalSummary(
             slice_timing=run_stc,
             registration=('FSL', 'FreeSurfer')[freesurfer],
-            registration_dof=bold2t1w_dof,
+            registration_dof=config.workflow.bold2t1w_dof,
             pe_direction=metadata.get("PhaseEncodingDirection"),
             tr=metadata.get("RepetitionTime")),
         name='summary', mem_gb=config.DEFAULT_MEMORY_MIN_GB, run_without_submitting=True)
-    summary.inputs.dummy_scans = dummy_scans
+    summary.inputs.dummy_scans = config.workflow.dummy_scans
 
     func_derivatives_wf = init_func_derivatives_wf(
         bids_root=layout.root,
-        cifti_output=cifti_output,
+        cifti_output=config.workflow.cifti_output,
         freesurfer=freesurfer,
         metadata=metadata,
-        output_dir=output_dir,
+        output_dir=config.execution.output_dir,
         spaces=spaces,
-        use_aroma=use_aroma,
+        use_aroma=config.workflow.use_aroma,
     )
 
     workflow.connect([
@@ -331,8 +307,8 @@ def init_func_preproc_wf(bold_file):
     ])
 
     # Generate a tentative boldref
-    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
-    bold_reference_wf.inputs.inputnode.dummy_scans = dummy_scans
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=config.nipype.omp_nthreads)
+    bold_reference_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
     if sbref_file is not None:
         workflow.connect([
             (val_sbref, bold_reference_wf, [('out_file', 'inputnode.sbref_file')]),
@@ -351,7 +327,7 @@ def init_func_preproc_wf(bold_file):
     bold_reg_wf = init_bold_reg_wf(name='bold_reg_wf',
                                    freesurfer=freesurfer,
                                    use_bbr=use_bbr,
-                                   bold2t1w_dof=bold2t1w_dof,
+                                   bold2t1w_dof=config.workflow.bold2t1w_dof,
                                    mem_gb=mem_gb['resampled'],
                                    omp_nthreads=omp_nthreads,
                                    use_compression=False)
@@ -369,9 +345,9 @@ def init_func_preproc_wf(bold_file):
     bold_confounds_wf = init_bold_confs_wf(
         mem_gb=mem_gb['largemem'],
         metadata=metadata,
-        regressors_all_comps=regressors_all_comps,
-        regressors_fd_th=regressors_fd_th,
-        regressors_dvars_th=regressors_dvars_th,
+        regressors_all_comps=config.workflow.regressors_all_comps,
+        regressors_fd_th=config.workflow.regressors_fd_th,
+        regressors_dvars_th=config.workflow.regressors_dvars_th,
         name='bold_confounds_wf')
     bold_confounds_wf.get_node('inputnode').inputs.t1_transform_flags = [False]
 
@@ -380,7 +356,7 @@ def init_func_preproc_wf(bold_file):
     bold_bold_trans_wf = init_bold_preproc_trans_wf(
         mem_gb=mem_gb['resampled'],
         omp_nthreads=omp_nthreads,
-        use_compression=not low_mem,
+        use_compression=not config.execution.low_mem,
         use_fieldwarp=bool(fmaps),
         name='bold_bold_trans_wf'
     )
@@ -413,7 +389,8 @@ def init_func_preproc_wf(bold_file):
 
     # SDC (SUSCEPTIBILITY DISTORTION CORRECTION) or bypass ##########################
     bold_sdc_wf = init_sdc_estimate_wf(fmaps, metadata,
-                                       omp_nthreads=omp_nthreads, debug=debug)
+                                       omp_nthreads=omp_nthreads,
+                                       debug=config.execution.debug)
 
     # MULTI-ECHO EPI DATA #############################################
     if multiecho:
@@ -650,7 +627,7 @@ def init_func_preproc_wf(bold_file):
             omp_nthreads=omp_nthreads,
             spaces=spaces,
             name='bold_std_trans_wf',
-            use_compression=not low_mem,
+            use_compression=not config.execution.low_mem,
             use_fieldwarp=bool(fmaps),
         )
         workflow.connect([
@@ -735,15 +712,15 @@ def init_func_preproc_wf(bold_file):
             ]),
         ])
 
-        if use_aroma:  # ICA-AROMA workflow
+        if config.workflow.use_aroma:  # ICA-AROMA workflow
             from .confounds import init_ica_aroma_wf
             ica_aroma_wf = init_ica_aroma_wf(
                 mem_gb=mem_gb['resampled'],
                 metadata=metadata,
                 omp_nthreads=omp_nthreads,
                 use_fieldwarp=bool(fmaps),
-                err_on_aroma_warn=err_on_aroma_warn,
-                aroma_melodic_dim=aroma_melodic_dim,
+                err_on_aroma_warn=config.workflow.aroma_err_on_warn,
+                aroma_melodic_dim=config.workflow.aroma_melodic_dim,
                 name='ica_aroma_wf')
 
             join = pe.Node(niu.Function(output_names=["out_file"],
@@ -799,7 +776,7 @@ def init_func_preproc_wf(bold_file):
         bold_surf_wf = init_bold_surf_wf(
             mem_gb=mem_gb['resampled'],
             surface_spaces=freesurfer_spaces,
-            medial_surface_nan=medial_surface_nan,
+            medial_surface_nan=config.workflow.medial_surface_nan,
             name='bold_surf_wf')
         workflow.connect([
             (inputnode, bold_surf_wf, [
@@ -814,10 +791,10 @@ def init_func_preproc_wf(bold_file):
         ])
 
         # CIFTI output
-        if cifti_output:
+        if config.workflow.cifti_output:
             from .resampling import init_bold_grayords_wf
             bold_grayords_wf = init_bold_grayords_wf(
-                grayord_density=cifti_output,
+                grayord_density=config.workflow.cifti_output,
                 mem_gb=mem_gb['resampled'],
                 repetition_time=metadata['RepetitionTime'])
 
@@ -839,6 +816,7 @@ def init_func_preproc_wf(bold_file):
             ])
 
     # REPORTING ############################################################
+    reportlets_dir = str(config.execution.work_dir / 'reportlets')
     ds_report_summary = pe.Node(
         DerivativesDataSink(desc='summary', keep_dtype=True),
         name='ds_report_summary', run_without_submitting=True,

From 08eb784c9957029a53155b2df53e0ae29fc5dc64 Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 5 Mar 2020 15:05:07 -0500
Subject: [PATCH 06/43] FIX: cli errors

---
 fmriprep/cli/parser.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index fafdc6936..d963e1102 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -278,7 +278,7 @@ def _bids_filter(value):
 
     latest = check_latest()
     if latest is not None and currentv < latest:
-        parser.warning("""\
+        config.loggers.cli.warning("""\
 You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.
 Please check out our documentation about how and when to upgrade:
 https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (
@@ -287,7 +287,7 @@ def _bids_filter(value):
     _blist = is_flagged()
     if _blist[0]:
         _reason = _blist[1] or 'unknown'
-        parser.warning("""\
+        config.loggers.cli.warning("""\
 WARNING: Version %s of fMRIPrep (current) has been FLAGGED
 (reason: %s).
 That means some severe flaw was found in it and we strongly
@@ -315,7 +315,7 @@ def parse_args(args=None, namespace=None):
 license file at several paths, in this order: 1) command line argument ``--fs-license-file``; \
 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \
 (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html""")
-    os.environ['FS_LICENSE'] = config.execution.fs_license_file
+    os.environ['FS_LICENSE'] = str(config.execution.fs_license_file)
 
     # Load base plugin_settings from file if --use-plugin
     if opts.use_plugin is not None:
@@ -355,14 +355,14 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
-        parser.error(
+        config.loggers.cli.error(
             'The selected output folder is the same as the input BIDS folder. '
             'Please modify the output path (suggestion: %s).'
             % bids_dir / 'derivatives' / ('fmriprep-%s' % version.split('+')[0])
         )
 
     if bids_dir in work_dir.parents:
-        parser.error(
+        config.loggers.cli.error(
             'The selected working directory is a subdirectory of the input BIDS folder. '
             'Please modify the output path.'
         )
@@ -388,7 +388,7 @@ def parse_args(args=None, namespace=None):
     participant_label = set(config.execution.participant_label)
     missing_subjects = participant_label - set(config.execution.layout.get_subjects())
     if missing_subjects:
-        parser.error(
+        config.loggers.cli.error(
             "One or more participant labels were not found in the BIDS directory: "
             "%s." % ", ".join(missing_subjects))
 

From 133f0e20efeee2e25fddc51ddecb55fd16e7182f Mon Sep 17 00:00:00 2001
From: mathiasg <mathiasg@stanford.edu>
Date: Thu, 5 Mar 2020 17:02:42 -0500
Subject: [PATCH 07/43] FIX: minor errors

---
 fmriprep/workflows/bold/base.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 7008145e0..3bc32873a 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -156,7 +156,7 @@ def init_func_preproc_wf(bold_file):
     layout = config.execution.layout
     omp_nthreads = config.nipype.omp_nthreads
     freesurfer = config.workflow.run_reconall
-    spaces = config.execution.output_spaces
+    spaces = config.workflow.spaces
 
     if multiecho:
         tes = [layout.get_metadata(echo)['EchoTime'] for echo in bold_file]
@@ -280,7 +280,7 @@ def init_func_preproc_wf(bold_file):
         cifti_output=config.workflow.cifti_output,
         freesurfer=freesurfer,
         metadata=metadata,
-        output_dir=config.execution.output_dir,
+        output_dir=str(config.execution.output_dir),
         spaces=spaces,
         use_aroma=config.workflow.use_aroma,
     )
@@ -326,7 +326,7 @@ def init_func_preproc_wf(bold_file):
     # calculate BOLD registration to T1w
     bold_reg_wf = init_bold_reg_wf(name='bold_reg_wf',
                                    freesurfer=freesurfer,
-                                   use_bbr=use_bbr,
+                                   use_bbr=config.workflow.use_bbr,
                                    bold2t1w_dof=config.workflow.bold2t1w_dof,
                                    mem_gb=mem_gb['resampled'],
                                    omp_nthreads=omp_nthreads,

From 2130726ca0bd2a96d6caa532292a2e81842c2d09 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:06:22 -0800
Subject: [PATCH 08/43] fix: map missing parameters from cli

---
 fmriprep/cli/parser.py          | 9 ++++++---
 fmriprep/workflows/bold/base.py | 2 +-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index d963e1102..b3368f743 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -183,16 +183,19 @@ def _bids_filter(value):
     # Confounds options
     g_confounds = parser.add_argument_group('Specific options for estimating confounds')
     g_confounds.add_argument(
-        '--return-all-components', required=False, action='store_true', default=False,
+        '--return-all-components', dest='regressors_all_comps', required=False,
+        action='store_true', default=False,
         help='Include all components estimated in CompCor decomposition in the confounds '
              'file instead of only the components sufficient to explain 50 percent of '
              'BOLD variance in each CompCor mask')
     g_confounds.add_argument(
-        '--fd-spike-threshold', required=False, action='store', default=0.5, type=float,
+        '--fd-spike-threshold', dest='regressors_fd_th', required=False,
+        action='store', default=0.5, type=float,
         help='Threshold for flagging a frame as an outlier on the basis of framewise '
              'displacement')
     g_confounds.add_argument(
-        '--dvars-spike-threshold', required=False, action='store', default=1.5, type=float,
+        '--dvars-spike-threshold', dest='regressors_dvars_th', required=False,
+        action='store', default=1.5, type=float,
         help='Threshold for flagging a frame as an outlier on the basis of standardised '
              'DVARS')
 
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 3bc32873a..a0be209e6 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -490,7 +490,7 @@ def init_func_preproc_wf(bold_file):
         (outputnode, summary, [('confounds', 'confounds_file')]),
     ])
 
-    if not t2s_coreg:
+    if not config.workflow.t2s_coreg:
         workflow.connect([
             (bold_sdc_wf, bold_reg_wf, [
                 ('outputnode.epi_brain', 'inputnode.ref_bold_brain')]),

From a48c66c594b1b394a07ba5555db08a57c94aaed6 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:15:03 -0800
Subject: [PATCH 09/43] fix: finalize porting

---
 fmriprep/cli/run.py | 24 ++++++++++++++++--------
 fmriprep/config.py  |  6 ++++--
 2 files changed, 20 insertions(+), 10 deletions(-)

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index cdb3ca29c..c539bbf78 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -99,8 +99,11 @@ def main():
     except Exception as e:
         if not config.execution.notrack:
             from ..utils.sentry import process_crashfile
-            crashfolders = [output_dir / 'fmriprep' / 'sub-{}'.format(s) / 'log' / run_uuid
-                            for s in subject_list]
+            crashfolders = [
+                config.execution.output_dir / 'fmriprep'
+                / 'sub-{}'.format(s) / 'log' / config.execution.run_uuid
+                for s in config.execution.participant_label
+            ]
             for crashfolder in crashfolders:
                 for crashfile in crashfolder.glob('crash*.*'):
                     process_crashfile(crashfile)
@@ -122,9 +125,9 @@ def main():
             from niworkflows.utils.misc import _copy_any
             dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
             _copy_any(dseg_tsv,
-                      str(output_dir / 'fmriprep' / 'desc-aseg_dseg.tsv'))
+                      str(config.execution.output_dir / 'fmriprep' / 'desc-aseg_dseg.tsv'))
             _copy_any(dseg_tsv,
-                      str(output_dir / 'fmriprep' / 'desc-aparcaseg_dseg.tsv'))
+                      str(config.execution.output_dir / 'fmriprep' / 'desc-aparcaseg_dseg.tsv'))
         errno = 0
     finally:
         from niworkflows.reports import generate_reports
@@ -133,8 +136,8 @@ def main():
         from shutil import copyfile
 
         citation_files = {
-            ext: output_dir / 'fmriprep' / 'logs' / ('CITATION.%s' % ext)
-            for ext in ('bib', 'tex', 'md', 'html')
+            ext: config.execution.output_dir.output_dir / 'fmriprep' / 'logs'
+            / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
         }
 
         if not config.execution.md_only_boilerplate and citation_files['md'].exists():
@@ -177,10 +180,15 @@ def main():
 
         # Generate reports phase
         failed_reports = generate_reports(
-            subject_list, output_dir, work_dir, run_uuid,
+            config.execution.participant_label,
+            config.execution.output_dir,
+            config.execution.work_dir,
+            config.execution.run_uuid,
             config=pkgrf('fmriprep', 'data/reports-spec.yml'),
             packagename='fmriprep')
-        write_derivative_description(bids_dir, output_dir / 'fmriprep')
+        write_derivative_description(
+            config.execution.bids_dir,
+            config.execution.output_dir / 'fmriprep')
 
         if failed_reports and not config.execution.notrack:
             sentry_sdk.capture_message(
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 951a27ed2..8e6591349 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -111,6 +111,7 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
 warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
 warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
 warnings.simplefilter('ignore', DeprecationWarning)
+warnings.simplefilter('ignore', FutureWarning)
 warnings.simplefilter('ignore', ResourceWarning)
 warnings.showwarning = redirect_warnings
 
@@ -230,8 +231,9 @@ def get_plugin(cls):
             'plugin_args': cls.plugin_args,
         }
         if cls.plugin in ('MultiProc', 'LegacyMultiProc'):
-            out['plugin_args']['nprocs'] = cls.nprocs
-            out['plugin_args']['memory_gb'] = cls.memory_gb
+            out['plugin_args']['nprocs'] = int(cls.nprocs)
+            if cls.memory_gb:
+                out['plugin_args']['memory_gb'] = float(cls.memory_gb)
         return out
 
 

From cc4796ec0eed6b9bcc0882d29dad3a4a29e42309 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:26:22 -0800
Subject: [PATCH 10/43] fix: trying to get ahold of warnings

---
 fmriprep/config.py | 23 +++++++++++------------
 1 file changed, 11 insertions(+), 12 deletions(-)

diff --git a/fmriprep/config.py b/fmriprep/config.py
index 8e6591349..2b9c4b3a3 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -98,22 +98,13 @@
 import warnings
 from multiprocessing import set_start_method
 
-
-def redirect_warnings(message, category, filename, lineno, file=None, line=None):
-    """Redirect other warnings."""
-    import logging
-    logger = logging.getLogger()
-    logger.debug('Captured warning (%s): %s', category, message)
-
-
 # cmp is not used by fmriprep, so ignore nipype-generated warnings
-warnings.filterwarnings('ignore', r'cmp not installed')
-warnings.filterwarnings('ignore', r'This has not been fully tested. Please report any failures.')
-warnings.filterwarnings('ignore', r"can't resolve package from __spec__ or __package__")
+warnings.filterwarnings('ignore', 'cmp not installed')
+warnings.filterwarnings('ignore', 'This has not been fully tested. Please report any failures.')
+warnings.filterwarnings('ignore', "can't resolve package from __spec__ or __package__")
 warnings.simplefilter('ignore', DeprecationWarning)
 warnings.simplefilter('ignore', FutureWarning)
 warnings.simplefilter('ignore', ResourceWarning)
-warnings.showwarning = redirect_warnings
 
 
 try:
@@ -135,6 +126,14 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
     from . import __version__
 
 
+def redirect_warnings(message, category, filename, lineno, file=None, line=None):
+    """Redirect other warnings."""
+    logger = logging.getLogger()
+    logger.debug('Captured warning (%s): %s', category, message)
+
+
+warnings.showwarning = redirect_warnings
+
 logging.addLevelName(25, 'IMPORTANT')  # Add a new level between INFO and WARNING
 logging.addLevelName(15, 'VERBOSE')  # Add a new level between INFO and DEBUG
 

From c7ceccf4d857867359fca4c5580e23a10a0c0ac8 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:26:36 -0800
Subject: [PATCH 11/43] fix: forgotten ubound variable

---
 fmriprep/workflows/bold/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index a0be209e6..0ae6a44c9 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -224,7 +224,7 @@ def init_func_preproc_wf(bold_file):
 
     # By default, force-bbr for t2s_coreg unless user specifies otherwise
     if config.workflow.t2s_coreg and config.workflow.use_bbr is None:
-        use_bbr = True
+        config.workflow.use_bbr.use_bbr = True
 
     # Build workflow
     workflow = Workflow(name=wf_name)

From 03e29d3ce6894de38123e46b391afbb1fec3b932 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:37:24 -0800
Subject: [PATCH 12/43] enh: use warning filters

---
 fmriprep/config.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/fmriprep/config.py b/fmriprep/config.py
index 2b9c4b3a3..ca076884f 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -102,9 +102,9 @@
 warnings.filterwarnings('ignore', 'cmp not installed')
 warnings.filterwarnings('ignore', 'This has not been fully tested. Please report any failures.')
 warnings.filterwarnings('ignore', "can't resolve package from __spec__ or __package__")
-warnings.simplefilter('ignore', DeprecationWarning)
-warnings.simplefilter('ignore', FutureWarning)
-warnings.simplefilter('ignore', ResourceWarning)
+warnings.filterwarnings('ignore', category=DeprecationWarning)
+warnings.filterwarnings('ignore', category=FutureWarning)
+warnings.filterwarnings('ignore', category=ResourceWarning)
 
 
 try:

From c3dc414f5d3f5d52ae72937bb85259c05d7609b7 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:52:47 -0800
Subject: [PATCH 13/43] fix: very minor fixes

---
 fmriprep/cli/run.py | 2 +-
 fmriprep/config.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index c539bbf78..1360e9849 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -136,7 +136,7 @@ def main():
         from shutil import copyfile
 
         citation_files = {
-            ext: config.execution.output_dir.output_dir / 'fmriprep' / 'logs'
+            ext: config.execution.output_dir / 'fmriprep' / 'logs'
             / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
         }
 
diff --git a/fmriprep/config.py b/fmriprep/config.py
index ca076884f..2fb59de95 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -95,8 +95,8 @@
       :py:class:`~bids.layout.BIDSLayout`
 
 """
-import warnings
 from multiprocessing import set_start_method
+import warnings
 
 # cmp is not used by fmriprep, so ignore nipype-generated warnings
 warnings.filterwarnings('ignore', 'cmp not installed')

From 9b03c310b8201178ec7b0e715e612e09dc49e2e6 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 14:55:02 -0800
Subject: [PATCH 14/43] pin: niworkflows dev

---
 setup.cfg | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.cfg b/setup.cfg
index 0c60f0840..40f2be6dd 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -23,7 +23,7 @@ install_requires =
     nibabel >= 3.0.1
     nipype >= 1.3.1
     nitime
-    niworkflows ~= 1.1.8
+    niworkflows @ git+https://github.com/nipreps/niworkflows.git@76f831f1f8fbf6c277fdf92535639bbf11d84527
     numpy
     pandas
     psutil >= 5.4

From 68bf9989014646a6c964815706e362708ee7accd Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 15:18:39 -0800
Subject: [PATCH 15/43] enh: keep track of templateflow home / demote some log
 traces

---
 fmriprep/config.py              | 12 ++++++++++++
 fmriprep/workflows/base.py      |  5 +++++
 fmriprep/workflows/bold/base.py |  9 ++++-----
 3 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/fmriprep/config.py b/fmriprep/config.py
index 2fb59de95..63a2fd7f1 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -123,6 +123,7 @@
     from time import strftime
     from niworkflows.utils.spaces import SpatialReferences as _SRs, Reference as _Ref
     from nipype import logging as nlogging, __version__ as _nipype_ver
+    from templateflow import __version__ as _tf_ver
     from . import __version__
 
 
@@ -154,6 +155,11 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
 if _fs_license is None and os.getenv('FREESURFER_HOME'):
     _fs_license = os.path.join(os.getenv('FREESURFER_HOME'), 'license.txt')
 
+_templateflow_home = Path(os.getenv(
+    'TEMPLATEFLOW_HOME',
+    os.path.join(os.getenv('HOME'), '.cache', 'templateflow'))
+)
+
 
 class _Config:
     """An abstract class forbidding instantiation."""
@@ -279,6 +285,9 @@ class execution(_Config):
     """List of participant identifiers that are to be preprocessed."""
     task_id = None
     """Select a particular task from all available in the dataset."""
+    templateflow_home = _templateflow_home
+    """The root folder of the TemplateFlow client."""
+    templateflow_version = _tf_ver
     version = __version__
     """*fMRIPrep*'s version."""
     work_dir = Path('work').absolute()
@@ -295,6 +304,7 @@ class execution(_Config):
         'layout',
         'log_dir',
         'output_dir',
+        'templateflow_home',
         'work_dir',
     )
 
@@ -303,6 +313,8 @@ class execution(_Config):
 del _fs_license
 del _exec_env
 del _nipype_ver
+del _templateflow_home
+del _tf_ver
 
 
 class workflow(_Config):
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 5584cb556..fe9e08f6e 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -295,6 +295,11 @@ def init_single_subject_wf(subject_id):
               ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')]),
         ])
 
+    # Dump a copy of the config file into the log directory
+    log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
+        / 'log' / config.execution.run_uuid
+    log_dir.mkdir(exist_ok=True, parents=True)
+    config.to_filename(log_dir / 'fmriprep.toml')
     return workflow
 
 
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 0ae6a44c9..1b596132f 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -166,9 +166,9 @@ def init_func_preproc_wf(bold_file):
         bold_tlen, mem_gb = _create_mem_gb(ref_file)
 
     wf_name = _get_wf_name(ref_file)
-    config.loggers.workflow.log(
-        25, ('Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
-             'Memory resampled/largemem=%.2f/%.2f GB.'),
+    config.loggers.workflow.debug(
+        'Creating bold processing workflow for "%s" (%.2f GB / %d TRs). '
+        'Memory resampled/largemem=%.2f/%.2f GB.',
         ref_file, mem_gb['filesize'], bold_tlen, mem_gb['resampled'], mem_gb['largemem'])
 
     sbref_file = None
@@ -771,8 +771,7 @@ def init_func_preproc_wf(bold_file):
     # Freesurfer
     freesurfer_spaces = spaces.get_fs_spaces()
     if freesurfer and freesurfer_spaces:
-        config.loggers.workflow.log(
-            25, 'Creating BOLD surface-sampling workflow.')
+        config.loggers.workflow.debug('Creating BOLD surface-sampling workflow.')
         bold_surf_wf = init_bold_surf_wf(
             mem_gb=mem_gb['resampled'],
             surface_spaces=freesurfer_spaces,

From b5ed669f122d3a42546dab65e9168d0f84aa03e5 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 16:17:05 -0800
Subject: [PATCH 16/43] fix: track more platform vars, integration with sentry

---
 fmriprep/cli/workflow.py |  6 ++++
 fmriprep/config.py       | 44 ++++++++++++++++++++++++++--
 fmriprep/utils/sentry.py | 63 +++++++---------------------------------
 3 files changed, 57 insertions(+), 56 deletions(-)

diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
index b3ccccf09..1c3a38b70 100644
--- a/fmriprep/cli/workflow.py
+++ b/fmriprep/cli/workflow.py
@@ -34,6 +34,12 @@ def build_workflow(config_file, retval):
     if msg is not None:
         build_log.warning(msg)
 
+    dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
+    if dset_desc_path.exists():
+        from hashlib import sha256
+        desc_content = dset_desc_path.read_bytes()
+        config.execution.bids_description_hash = sha256(desc_content).hexdigest()
+
     # First check that bids_dir looks like a BIDS folder
     config.init_layout()
     subject_list = collect_participants(
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 63a2fd7f1..a77d20753 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -141,14 +141,14 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
 DEFAULT_MEMORY_MIN_GB = 0.01
 
 _exec_env = os.name
+_docker_ver = None
 # special variable set in the container
 if os.getenv('IS_DOCKER_8395080871'):
     _exec_env = 'singularity'
     _cgroup = Path('/proc/1/cgroup')
     if _cgroup.exists() and 'docker' in _cgroup.read_text():
-        _exec_env = 'docker'
-        if os.getenv('DOCKER_VERSION_8395080871'):
-            _exec_env = 'fmriprep-docker'
+        _docker_ver = os.getenv('DOCKER_VERSION_8395080871')
+        _exec_env = 'fmriprep-docker' if _docker_ver else 'docker'
     del _cgroup
 
 _fs_license = os.getenv('FS_LICENSE')
@@ -160,6 +160,32 @@ def redirect_warnings(message, category, filename, lineno, file=None, line=None)
     os.path.join(os.getenv('HOME'), '.cache', 'templateflow'))
 )
 
+try:
+    from psutil import virtual_memory
+    _free_mem_at_start = round(virtual_memory().free / 1024**3, 1)
+except Exception:
+    _free_mem_at_start = None
+
+_oc_limit = 'n/a'
+_oc_policy = 'n/a'
+try:
+    # Memory policy may have a large effect on types of errors experienced
+    _proc_oc_path = Path('/proc/sys/vm/overcommit_memory')
+    if _proc_oc_path.exists():
+        _oc_policy = {
+            '0': 'heuristic', '1': 'always', '2': 'never'
+        }.get(_proc_oc_path.read_text().strip(), 'unknown')
+        if _oc_policy != 'never':
+            _proc_oc_kbytes = Path('/proc/sys/vm/overcommit_kbytes')
+            if _proc_oc_kbytes.exists():
+                _oc_limit = _proc_oc_kbytes.read_text().strip()
+            if _oc_limit in ('0', 'n/a') and Path('/proc/sys/vm/overcommit_ratio').exists():
+                _oc_limit = '{}%'.format(
+                    Path('/proc/sys/vm/overcommit_ratio').read_text().strip()
+                )
+except Exception:
+    pass
+
 
 class _Config:
     """An abstract class forbidding instantiation."""
@@ -206,6 +232,8 @@ class nipype(_Config):
 
     crashfile_format = 'txt'
     """The file format for crashfiles, either text or pickle."""
+    free_mem = _free_mem_at_start
+    """Free memory at start."""
     get_linked_libs = False
     """Run NiPype's tool to enlist linked libraries for every interface."""
     memory_gb = None
@@ -214,6 +242,10 @@ class nipype(_Config):
     """Number of processes (compute tasks) that can be run in parallel (multiprocessing only)."""
     omp_nthreads = os.cpu_count()
     """Number of CPUs a single process can access for multithreaded execution."""
+    overcommit_policy = _oc_policy
+    """Linux's kernel virtual memory overcommit policy."""
+    overcommit_limit = _oc_limit
+    """Linux's kernel virtual memory overcommit limits."""
     plugin = 'MultiProc'
     """NiPype's execution plugin."""
     plugin_args = {
@@ -255,6 +287,8 @@ class execution(_Config):
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
     echo_idx = None
     """Select a particular echo for multi-echo EPI datasets."""
+    exec_docker_version = _docker_ver
+    """Version of Docker Engine."""
     exec_env = _exec_env
     """A string representing the execution platform."""
     fs_license_file = _fs_license
@@ -288,6 +322,7 @@ class execution(_Config):
     templateflow_home = _templateflow_home
     """The root folder of the TemplateFlow client."""
     templateflow_version = _tf_ver
+    """The TemplateFlow client version installed."""
     version = __version__
     """*fMRIPrep*'s version."""
     work_dir = Path('work').absolute()
@@ -315,6 +350,9 @@ class execution(_Config):
 del _nipype_ver
 del _templateflow_home
 del _tf_ver
+del _free_mem_at_start
+del _oc_limit
+del _oc_policy
 
 
 class workflow(_Config):
diff --git a/fmriprep/utils/sentry.py b/fmriprep/utils/sentry.py
index c383afed8..f7f406a48 100644
--- a/fmriprep/utils/sentry.py
+++ b/fmriprep/utils/sentry.py
@@ -1,8 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
-"""Stripped out routines for Sentry"""
+"""Stripped out routines for Sentry."""
 import os
-from pathlib import Path
 import re
 from niworkflows.utils.misc import read_crashfile
 import sentry_sdk
@@ -43,66 +42,24 @@
 
 
 def sentry_setup():
-    from os import cpu_count
-    import psutil
-    import hashlib
-
-    exec_env = config.execution.exec_env
-    environment = "prod"
-    release = config.execution.version
-    if not release:
-        environment = "dev"
-        release = "dev"
-    elif int(os.getenv('FMRIPREP_DEV', '0')) or ('+' in release):
-        environment = "dev"
+    """Set-up sentry."""
+    release = config.execution.version or "dev"
+    environment = "dev" if (
+        os.getenv('FMRIPREP_DEV', '').lower in ('1', 'on', 'yes', 'y', 'true')
+        or ('+' in release)
+    ) else "prod"
 
     sentry_sdk.init("https://d5a16b0c38d84d1584dfc93b9fb1ade6@sentry.io/1137693",
                     release=release,
                     environment=environment,
                     before_send=before_send)
     with sentry_sdk.configure_scope() as scope:
-        scope.set_tag('exec_env', exec_env)
-
-        if exec_env == 'fmriprep-docker':
-            scope.set_tag('docker_version', os.getenv('DOCKER_VERSION_8395080871'))
-
-        dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
-        if dset_desc_path.exists():
-            desc_content = dset_desc_path.read_bytes()
-            scope.set_tag('dset_desc_sha256', hashlib.sha256(desc_content).hexdigest())
-
-        free_mem_at_start = round(psutil.virtual_memory().free / 1024**3, 1)
-        scope.set_tag('free_mem_at_start', free_mem_at_start)
-        scope.set_tag('cpu_count', cpu_count())
-
-        # Memory policy may have a large effect on types of errors experienced
-        overcommit_memory = Path('/proc/sys/vm/overcommit_memory')
-        if overcommit_memory.exists():
-            policy = {'0': 'heuristic',
-                      '1': 'always',
-                      '2': 'never'}.get(overcommit_memory.read_text().strip(), 'unknown')
-            scope.set_tag('overcommit_memory', policy)
-            if policy == 'never':
-                overcommit_kbytes = Path('/proc/sys/vm/overcommit_memory')
-                kb = overcommit_kbytes.read_text().strip()
-                if kb != '0':
-                    limit = '{}kB'.format(kb)
-                else:
-                    overcommit_ratio = Path('/proc/sys/vm/overcommit_ratio')
-                    limit = '{}%'.format(overcommit_ratio.read_text().strip())
-                scope.set_tag('overcommit_limit', limit)
-            else:
-                scope.set_tag('overcommit_limit', 'n/a')
-        else:
-            scope.set_tag('overcommit_memory', 'n/a')
-            scope.set_tag('overcommit_limit', 'n/a')
-
         for k, v in config.get(flat=True).items():
             scope.set_tag(k, v)
 
 
 def process_crashfile(crashfile):
-    """Parse the contents of a crashfile and submit sentry messages"""
+    """Parse the contents of a crashfile and submit sentry messages."""
     crash_info = read_crashfile(str(crashfile))
     with sentry_sdk.push_scope() as scope:
         scope.level = 'fatal'
@@ -169,7 +126,7 @@ def process_crashfile(crashfile):
 
 
 def before_send(event, hints):
-    # Filtering log messages about crashed nodes
+    """Filter log messages about crashed nodes."""
     if 'logentry' in event and 'message' in event['logentry']:
         msg = event['logentry']['message']
         if msg.startswith("could not run node:"):
@@ -193,7 +150,7 @@ def before_send(event, hints):
 
 def _chunks(string, length=CHUNK_SIZE):
     """
-    Splits a string into smaller chunks
+    Split a string into smaller chunks.
 
     >>> list(_chunks('some longer string.', length=3))
     ['som', 'e l', 'ong', 'er ', 'str', 'ing', '.']

From 2c4de8b1d95747043ba7b5c43ef322f80f3659b8 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Thu, 5 Mar 2020 17:07:49 -0800
Subject: [PATCH 17/43] fix: sort out loggging, run boilerplate's md -> html
 isolated in process

---
 fmriprep/cli/run.py             | 57 +++++++--------------------------
 fmriprep/cli/workflow.py        | 47 ++++++++++++++++++++++++---
 fmriprep/config.py              |  8 +++++
 fmriprep/workflows/bold/base.py |  8 ++---
 4 files changed, 65 insertions(+), 55 deletions(-)

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index 1360e9849..4e1073a46 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -93,6 +93,9 @@ def main():
         sentry_sdk.capture_message('fMRIPrep started', level='info')
 
     config.loggers.workflow.log(25, 'fMRIPrep started!')
+    config.loggers.workflow.log(15, '\n'.join(
+        ['fMRIPrep config:'] + ['\t\t%s' % s for s in config.dumps().splitlines()])
+    )
     errno = 1  # Default is error exit unless otherwise set
     try:
         fmriprep_wf.run(**config.nipype.get_plugin())
@@ -113,13 +116,20 @@ def main():
         config.loggers.workflow.critical('fMRIPrep failed: %s', e)
         raise
     else:
-
         config.loggers.workflow.log(25, 'fMRIPrep finished successfully!')
         if not config.execution.notrack:
             success_message = 'fMRIPrep finished without errors'
             sentry_sdk.add_breadcrumb(message=success_message, level='info')
             sentry_sdk.capture_message(success_message, level='info')
 
+        # Bother users with the boilerplate only iff the workflow went okay.
+        if (config.execution.output_dir / 'fmriprep' / 'logs' / 'CITATION.md').exists():
+            config.loggers.workflow.log(
+                25, 'Works derived from this fMRIPrep execution should '
+                'include the following boilerplate:\n\n%s',
+                (config.execution.output_dir / 'fmriprep' / 'logs' / 'CITATION.md').read_text()
+            )
+
         if config.workflow.run_reconall:
             from templateflow import api
             from niworkflows.utils.misc import _copy_any
@@ -131,52 +141,7 @@ def main():
         errno = 0
     finally:
         from niworkflows.reports import generate_reports
-        from subprocess import check_call, CalledProcessError, TimeoutExpired
         from pkg_resources import resource_filename as pkgrf
-        from shutil import copyfile
-
-        citation_files = {
-            ext: config.execution.output_dir / 'fmriprep' / 'logs'
-            / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
-        }
-
-        if not config.execution.md_only_boilerplate and citation_files['md'].exists():
-            # Generate HTML file resolving citations
-            cmd = ['pandoc', '-s', '--bibliography',
-                   pkgrf('fmriprep', 'data/boilerplate.bib'),
-                   '--filter', 'pandoc-citeproc',
-                   '--metadata', 'pagetitle="fMRIPrep citation boilerplate"',
-                   str(citation_files['md']),
-                   '-o', str(citation_files['html'])]
-
-            config.loggers.cli.info(
-                'Generating an HTML version of the citation boilerplate...')
-            try:
-                check_call(cmd, timeout=10)
-            except (FileNotFoundError, CalledProcessError, TimeoutExpired):
-                config.loggers.cli.warning(
-                    'Could not generate CITATION.html file:\n%s', ' '.join(cmd))
-
-            # Generate LaTex file resolving citations
-            cmd = ['pandoc', '-s', '--bibliography',
-                   pkgrf('fmriprep', 'data/boilerplate.bib'),
-                   '--natbib', str(citation_files['md']),
-                   '-o', str(citation_files['tex'])]
-            config.loggers.cli.info(
-                'Generating a LaTeX version of the citation boilerplate...')
-            try:
-                check_call(cmd, timeout=10)
-            except (FileNotFoundError, CalledProcessError, TimeoutExpired):
-                config.loggers.cli.warning(
-                    'Could not generate CITATION.tex file:\n%s', ' '.join(cmd))
-            else:
-                copyfile(pkgrf('fmriprep', 'data/boilerplate.bib'),
-                         citation_files['bib'])
-        else:
-            config.loggers.cli.warning(
-                'fMRIPrep could not find the markdown version of '
-                'the citation boilerplate (%s). HTML and LaTeX versions'
-                ' of it will not be available', citation_files['md'])
 
         # Generate reports phase
         failed_reports = generate_reports(
diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
index 1c3a38b70..43ce7d24c 100644
--- a/fmriprep/cli/workflow.py
+++ b/fmriprep/cli/workflow.py
@@ -121,8 +121,45 @@ def build_boilerplate(config_file, workflow):
             except FileNotFoundError:
                 pass
 
-        citation_files['md'].write_text(boilerplate)
-        config.loggers.workflow.log(
-            25, 'Works derived from this fMRIPrep execution should '
-            'include the following boilerplate:\n\n%s', boilerplate
-        )
+    citation_files['md'].write_text(boilerplate)
+
+    citation_files = {
+        ext: config.execution.output_dir / 'fmriprep' / 'logs'
+        / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
+    }
+
+    if not config.execution.md_only_boilerplate and citation_files['md'].exists():
+        from subprocess import check_call, CalledProcessError, TimeoutExpired
+        from pkg_resources import resource_filename as pkgrf
+        from shutil import copyfile
+        # Generate HTML file resolving citations
+        cmd = ['pandoc', '-s', '--bibliography',
+               pkgrf('fmriprep', 'data/boilerplate.bib'),
+               '--filter', 'pandoc-citeproc',
+               '--metadata', 'pagetitle="fMRIPrep citation boilerplate"',
+               str(citation_files['md']),
+               '-o', str(citation_files['html'])]
+
+        config.loggers.cli.info(
+            'Generating an HTML version of the citation boilerplate...')
+        try:
+            check_call(cmd, timeout=10)
+        except (FileNotFoundError, CalledProcessError, TimeoutExpired):
+            config.loggers.cli.warning(
+                'Could not generate CITATION.html file:\n%s', ' '.join(cmd))
+
+        # Generate LaTex file resolving citations
+        cmd = ['pandoc', '-s', '--bibliography',
+               pkgrf('fmriprep', 'data/boilerplate.bib'),
+               '--natbib', str(citation_files['md']),
+               '-o', str(citation_files['tex'])]
+        config.loggers.cli.info(
+            'Generating a LaTeX version of the citation boilerplate...')
+        try:
+            check_call(cmd, timeout=10)
+        except (FileNotFoundError, CalledProcessError, TimeoutExpired):
+            config.loggers.cli.warning(
+                'Could not generate CITATION.tex file:\n%s', ' '.join(cmd))
+        else:
+            copyfile(pkgrf('fmriprep', 'data/boilerplate.bib'),
+                     citation_files['bib'])
diff --git a/fmriprep/config.py b/fmriprep/config.py
index a77d20753..c8dc3998f 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -412,6 +412,9 @@ class workflow(_Config):
 class loggers(_Config):
     """Configure loggers."""
 
+    _fmt = "%(asctime)s,%(msecs)d %(name)-2s " "%(levelname)-2s:\n\t %(message)s"
+    _datefmt = "%y%m%d-%H:%M:%S"
+
     default = logging.getLogger()
     cli = logging.getLogger('cli')
     workflow = nlogging.getLogger('nipype.workflow')
@@ -485,6 +488,11 @@ def init_layout():
 
 def set_logger_level():
     """Set the current log level to all nipype loggers."""
+    _handler = logging.StreamHandler(stream=sys.stdout)
+    _handler.setFormatter(
+        logging.Formatter(fmt=loggers._fmt, datefmt=loggers._datefmt)
+    )
+    loggers.cli.addHandler(_handler)
     loggers.default.setLevel(execution.log_level)
     loggers.cli.setLevel(execution.log_level)
     loggers.interface.setLevel(execution.log_level)
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 1b596132f..ab3b1f0b4 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -192,11 +192,11 @@ def init_func_preproc_wf(bold_file):
                 "Multiple single-band reference files found for {}; using "
                 "{}".format(refbase, sbbase))
         else:
-            config.loggers.workflow.log(
-                25, "Using single-band reference file {}".format(sbbase))
+            config.loggers.workflow.info("Using single-band reference file %s.",
+                                         sbbase)
     else:
-        config.loggers.workflow.log(
-            25, "No single-band-reference found for {}".format(refbase))
+        config.loggers.workflow.info("No single-band-reference found for %s.",
+                                     refbase)
 
     metadata = layout.get_metadata(ref_file)
 

From ddfef28a47c2453d981e8dc4d770eb07941cbfcd Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 09:51:33 -0800
Subject: [PATCH 18/43] fix(tests): revise old parser tests and relocate
 properly

---
 fmriprep/cli/parser.py            |  9 +++---
 fmriprep/cli/tests/test_parser.py | 48 +++++++++++++++++++++++++++++
 fmriprep/cli/tests/test_run.py    | 51 -------------------------------
 3 files changed, 53 insertions(+), 55 deletions(-)
 delete mode 100644 fmriprep/cli/tests/test_run.py

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index b3368f743..117bd80d2 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -2,6 +2,7 @@
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Parser."""
 import os
+import sys
 from .. import config
 
 
@@ -281,20 +282,20 @@ def _bids_filter(value):
 
     latest = check_latest()
     if latest is not None and currentv < latest:
-        config.loggers.cli.warning("""\
+        print("""\
 You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.
 Please check out our documentation about how and when to upgrade:
 https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (
-            config.execution.version, latest))
+            currentv, latest), file=sys.stderr)
 
     _blist = is_flagged()
     if _blist[0]:
         _reason = _blist[1] or 'unknown'
-        config.loggers.cli.warning("""\
+        print("""\
 WARNING: Version %s of fMRIPrep (current) has been FLAGGED
 (reason: %s).
 That means some severe flaw was found in it and we strongly
-discourage its usage.""" % (config.execution.version, _reason))
+discourage its usage.""" % (config.execution.version, _reason), file=sys.stderr)
 
     return parser
 
diff --git a/fmriprep/cli/tests/test_parser.py b/fmriprep/cli/tests/test_parser.py
index 1781a725f..b9945d721 100644
--- a/fmriprep/cli/tests/test_parser.py
+++ b/fmriprep/cli/tests/test_parser.py
@@ -1,6 +1,9 @@
 """Test parser."""
+from packaging.version import Version
 import pytest
 from ..parser import _build_parser
+from .. import version as _version
+from ... import config
 
 MIN_ARGS = ['data/', 'out/', 'participant']
 
@@ -66,3 +69,48 @@ def test_memory_arg(tmp_path, argval, gb):
     opts = _build_parser().parse_args(args)
 
     assert opts.memory_gb == gb
+
+
+@pytest.mark.parametrize('current,latest', [
+    ('1.0.0', '1.3.2'),
+    ('1.3.2', '1.3.2')
+])
+def test_get_parser_update(monkeypatch, capsys, current, latest):
+    """Make sure the out-of-date banner is shown."""
+    expectation = Version(current) < Version(latest)
+
+    def _mock_check_latest(*args, **kwargs):
+        return Version(latest)
+
+    monkeypatch.setattr(config.execution, 'version', current)
+    monkeypatch.setattr(_version, 'check_latest', _mock_check_latest)
+
+    _build_parser()
+    captured = capsys.readouterr().err
+
+    msg = """\
+You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.
+Please check out our documentation about how and when to upgrade:
+https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (current, latest)
+
+    assert (msg in captured) is expectation
+
+
+@pytest.mark.parametrize('flagged', [
+    (True, None),
+    (True, 'random reason'),
+    (False, None),
+])
+def test_get_parser_blacklist(monkeypatch, capsys, flagged):
+    """Make sure the blacklisting banner is shown."""
+    def _mock_is_bl(*args, **kwargs):
+        return flagged
+
+    monkeypatch.setattr(_version, 'is_flagged', _mock_is_bl)
+
+    _build_parser()
+    captured = capsys.readouterr().err
+
+    assert ('FLAGGED' in captured) is flagged[0]
+    if flagged[0]:
+        assert ((flagged[1] or 'reason: unknown') in captured)
diff --git a/fmriprep/cli/tests/test_run.py b/fmriprep/cli/tests/test_run.py
deleted file mode 100644
index a4d90f200..000000000
--- a/fmriprep/cli/tests/test_run.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""Test CLI."""
-from packaging.version import Version
-import pytest
-from .. import version as _version
-from ... import __about__
-from ..run import get_parser
-
-
-@pytest.mark.parametrize(('current', 'latest'), [
-    ('1.0.0', '1.3.2'),
-    ('1.3.2', '1.3.2')
-])
-def test_get_parser_update(monkeypatch, capsys, current, latest):
-    """Make sure the out-of-date banner is shown."""
-    expectation = Version(current) < Version(latest)
-
-    def _mock_check_latest(*args, **kwargs):
-        return Version(latest)
-
-    monkeypatch.setattr(__about__, '__version__', current)
-    monkeypatch.setattr(_version, 'check_latest', _mock_check_latest)
-
-    get_parser()
-    captured = capsys.readouterr().err
-
-    msg = """\
-You are using fMRIPrep-%s, and a newer version of fMRIPrep is available: %s.
-Please check out our documentation about how and when to upgrade:
-https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading""" % (current, latest)
-
-    assert (msg in captured) is expectation
-
-
-@pytest.mark.parametrize('flagged', [
-    (True, None),
-    (True, 'random reason'),
-    (False, None),
-])
-def test_get_parser_blacklist(monkeypatch, capsys, flagged):
-    """Make sure the blacklisting banner is shown."""
-    def _mock_is_bl(*args, **kwargs):
-        return flagged
-
-    monkeypatch.setattr(_version, 'is_flagged', _mock_is_bl)
-
-    get_parser()
-    captured = capsys.readouterr().err
-
-    assert ('FLAGGED' in captured) is flagged[0]
-    if flagged[0]:
-        assert ((flagged[1] or 'reason: unknown') in captured)

From b729f20a38530f498386b086036a8e4e0d617649 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 10:01:03 -0800
Subject: [PATCH 19/43] fix: participant_labels is None error / better location
 for config file

---
 fmriprep/cli/parser.py     |  6 +++++-
 fmriprep/cli/workflow.py   |  3 ++-
 fmriprep/workflows/base.py | 16 +++++++---------
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 117bd80d2..cf7799b40 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -389,8 +389,12 @@ def parse_args(args=None, namespace=None):
 
     # First check that bids_dir looks like a BIDS folder
     config.init_layout()
+    all_subjects = config.execution.layout.get_subjects()
+    if config.execution.participant_label is None:
+        config.execution.participant_label = all_subjects
+
     participant_label = set(config.execution.participant_label)
-    missing_subjects = participant_label - set(config.execution.layout.get_subjects())
+    missing_subjects = participant_label - set(all_subjects)
     if missing_subjects:
         config.loggers.cli.error(
             "One or more participant labels were not found in the BIDS directory: "
diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
index 43ce7d24c..a410f49a5 100644
--- a/fmriprep/cli/workflow.py
+++ b/fmriprep/cli/workflow.py
@@ -27,13 +27,14 @@ def build_workflow(config_file, retval):
     retval['return_code'] = 1
     retval['workflow'] = None
 
-    # warn if older results exist
+    # warn if older results exist: check for dataset_description.json in output folder
     msg = check_pipeline_version(
         version, output_dir / 'fmriprep' / 'dataset_description.json'
     )
     if msg is not None:
         build_log.warning(msg)
 
+    # Please note this is the input folder's dataset_description.json
     dset_desc_path = config.execution.bids_dir / 'dataset_description.json'
     if dset_desc_path.exists():
         from hashlib import sha256
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index fe9e08f6e..436f2706f 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -86,6 +86,12 @@ def init_fmriprep_wf():
         else:
             fmriprep_wf.add_nodes([single_subject_wf])
 
+        # Dump a copy of the config file into the log directory
+        log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
+            / 'log' / config.execution.run_uuid
+        log_dir.mkdir(exist_ok=True, parents=True)
+        config.to_filename(log_dir / 'fmriprep.toml')
+
     return fmriprep_wf
 
 
@@ -294,19 +300,11 @@ def init_single_subject_wf(subject_id):
               ('outputnode.t1w2fsnative_xfm', 'inputnode.t1w2fsnative_xfm'),
               ('outputnode.fsnative2t1w_xfm', 'inputnode.fsnative2t1w_xfm')]),
         ])
-
-    # Dump a copy of the config file into the log directory
-    log_dir = config.execution.output_dir / 'fmriprep' / 'sub-{}'.format(subject_id) \
-        / 'log' / config.execution.run_uuid
-    log_dir.mkdir(exist_ok=True, parents=True)
-    config.to_filename(log_dir / 'fmriprep.toml')
     return workflow
 
 
 def _prefix(subid):
-    if subid.startswith('sub-'):
-        return subid
-    return '-'.join(('sub', subid))
+    return '-'.join(('sub', subid.lstrip('sub-')))
 
 
 def _pop(inlist):

From cb4506bbe07dad013f5b89d1990a6e1413816e93 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 11:07:59 -0800
Subject: [PATCH 20/43] enh: add a read-only section ``environment``

---
 fmriprep/cli/parser.py     | 12 ++++----
 fmriprep/cli/workflow.py   |  4 +--
 fmriprep/config.py         | 63 +++++++++++++++++++++++++-------------
 fmriprep/utils/sentry.py   |  2 +-
 fmriprep/workflows/base.py |  6 ++--
 5 files changed, 53 insertions(+), 34 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index cf7799b40..5a1ca00a8 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -46,12 +46,12 @@ def _bids_filter(value):
         if value and Path(value).exists():
             return loads(Path(value).read_text())
 
-    verstr = 'fMRIPrep v{}'.format(config.execution.version)
-    currentv = Version(config.execution.version)
+    verstr = 'fMRIPrep v{}'.format(config.environment.version)
+    currentv = Version(config.environment.version)
     is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
 
     parser = ArgumentParser(
-        description='fMRIPrep: fMRI PREProcessing workflows v{}'.format(config.execution.version),
+        description='fMRIPrep: fMRI PREProcessing workflows v{}'.format(config.environment.version),
         formatter_class=ArgumentDefaultsHelpFormatter)
     PathExists = partial(_path_exists, parser=parser)
     PositiveInt = partial(_min_one, parser=parser)
@@ -295,7 +295,7 @@ def _bids_filter(value):
 WARNING: Version %s of fMRIPrep (current) has been FLAGGED
 (reason: %s).
 That means some severe flaw was found in it and we strongly
-discourage its usage.""" % (config.execution.version, _reason), file=sys.stderr)
+discourage its usage.""" % (config.environment.version, _reason), file=sys.stderr)
 
     return parser
 
@@ -343,7 +343,7 @@ def parse_args(args=None, namespace=None):
     bids_dir = config.execution.bids_dir
     output_dir = config.execution.output_dir
     work_dir = config.execution.work_dir
-    version = config.execution.version
+    version = config.environment.version
 
     if config.execution.fs_subjects_dir is None:
         config.execution.fs_subjects_dir = output_dir / 'freesurfer'
@@ -378,7 +378,7 @@ def parse_args(args=None, namespace=None):
             "Making sure the input data is BIDS compliant (warnings can be ignored in most "
             "cases)."
         )
-        validate_input_dir(config.execution.exec_env, opts.bids_dir, opts.participant_label)
+        validate_input_dir(config.environment.exec_env, opts.bids_dir, opts.participant_label)
 
     # Setup directories
     config.execution.log_dir = output_dir / 'fmriprep' / 'logs'
diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
index a410f49a5..af2bbf120 100644
--- a/fmriprep/cli/workflow.py
+++ b/fmriprep/cli/workflow.py
@@ -22,7 +22,7 @@ def build_workflow(config_file, retval):
     build_log = config.loggers.workflow
 
     output_dir = config.execution.output_dir
-    version = config.execution.version
+    version = config.environment.version
 
     retval['return_code'] = 1
     retval['workflow'] = None
@@ -71,7 +71,7 @@ def build_workflow(config_file, retval):
       * Output spaces: {spaces}.
     """.format
     build_log.log(25, INIT_MSG(
-        version=config.execution.version,
+        version=config.environment.version,
         bids_dir=config.execution.bids_dir,
         subject_list=subject_list,
         uuid=config.execution.run_uuid,
diff --git a/fmriprep/config.py b/fmriprep/config.py
index c8dc3998f..59d4f474f 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -24,6 +24,16 @@
 The module also has a :py:func:`to_filename` function to allow writting out
 the settings to hard disk in *ToML* format, which looks like::
 
+    [environment]
+    cpu_count = 8
+    exec_env = "posix"
+    free_mem = 2.2
+    overcommit_policy = "heuristic"
+    overcommit_limit = "50%"
+    nipype_version = "1.5.0"
+    templateflow_version = "0.4.2"
+    version = "20.0.1"
+
     [nipype]
     crashfile_format = "txt"
     get_linked_libs = false
@@ -32,7 +42,6 @@
     plugin = "MultiProc"
     resource_monitor = false
     stop_on_first_crash = false
-    version = "1.5.0-dev+gdffcb7815"
 
     [execution]
     bids_dir = "/data/openfmri/ds000005"
@@ -49,8 +58,7 @@
     reports_only = false
     run_uuid = "20200302-174345_9ba9f304-82de-4538-8c3a-570c5f5d8f2f"
     participant_label = [ "01",]
-    version = "20.0.1+13.g3ca42930.dirty"
-    work_dir = "/home/oesteban/tmp/fmriprep-ds005/fprep-work2"
+    work_dir = "work/"
     write_graph = false
 
     [workflow]
@@ -227,13 +235,34 @@ def get(cls):
         return out
 
 
+class environment(_Config):
+    """Read-only options."""
+
+    cpu_count = os.cpu_count()
+    """Number of available CPUs."""
+    exec_docker_version = _docker_ver
+    """Version of Docker Engine."""
+    exec_env = _exec_env
+    """A string representing the execution platform."""
+    free_mem = _free_mem_at_start
+    """Free memory at start."""
+    overcommit_policy = _oc_policy
+    """Linux's kernel virtual memory overcommit policy."""
+    overcommit_limit = _oc_limit
+    """Linux's kernel virtual memory overcommit limits."""
+    nipype_version = _nipype_ver
+    """Nipype's current version."""
+    templateflow_version = _tf_ver
+    """The TemplateFlow client version installed."""
+    version = __version__
+    """*fMRIPrep*'s version."""
+
+
 class nipype(_Config):
     """Nipype configuration."""
 
     crashfile_format = 'txt'
     """The file format for crashfiles, either text or pickle."""
-    free_mem = _free_mem_at_start
-    """Free memory at start."""
     get_linked_libs = False
     """Run NiPype's tool to enlist linked libraries for every interface."""
     memory_gb = None
@@ -242,10 +271,6 @@ class nipype(_Config):
     """Number of processes (compute tasks) that can be run in parallel (multiprocessing only)."""
     omp_nthreads = os.cpu_count()
     """Number of CPUs a single process can access for multithreaded execution."""
-    overcommit_policy = _oc_policy
-    """Linux's kernel virtual memory overcommit policy."""
-    overcommit_limit = _oc_limit
-    """Linux's kernel virtual memory overcommit limits."""
     plugin = 'MultiProc'
     """NiPype's execution plugin."""
     plugin_args = {
@@ -257,8 +282,6 @@ class nipype(_Config):
     """Enable resource monitor."""
     stop_on_first_crash = True
     """Whether the workflow should stop or continue after the first error."""
-    version = _nipype_ver
-    """Nipype's current version."""
 
     @classmethod
     def get_plugin(cls):
@@ -279,6 +302,8 @@ class execution(_Config):
 
     bids_dir = None
     """An existing path to the dataset, which must be BIDS-compliant."""
+    bids_description_hash = None
+    """Checksum (SHA256) of the ``dataset_description.json`` of the BIDS dataset."""
     bids_filters = None
     """A dictionary of BIDS selection filters."""
     boilerplate_only = False
@@ -287,10 +312,6 @@ class execution(_Config):
     """Run in sloppy mode (meaning, suboptimal parameters that minimize run-time)."""
     echo_idx = None
     """Select a particular echo for multi-echo EPI datasets."""
-    exec_docker_version = _docker_ver
-    """Version of Docker Engine."""
-    exec_env = _exec_env
-    """A string representing the execution platform."""
     fs_license_file = _fs_license
     """An existing file containing a FreeSurfer license."""
     fs_subjects_dir = None
@@ -321,10 +342,6 @@ class execution(_Config):
     """Select a particular task from all available in the dataset."""
     templateflow_home = _templateflow_home
     """The root folder of the TemplateFlow client."""
-    templateflow_version = _tf_ver
-    """The TemplateFlow client version installed."""
-    version = __version__
-    """*fMRIPrep*'s version."""
     work_dir = Path('work').absolute()
     """Path to a working directory where intermediate results will be available."""
     write_graph = False
@@ -436,8 +453,9 @@ def load(filename):
     filename = Path(filename)
     settings = loads(filename.read_text())
     for sectionname, configs in settings.items():
-        section = getattr(sys.modules[__name__], sectionname)
-        section.load(configs)
+        if sectionname != 'environment':
+            section = getattr(sys.modules[__name__], sectionname)
+            section.load(configs)
     set_logger_level()
     init_spaces()
     init_layout()
@@ -446,9 +464,10 @@ def load(filename):
 def get(flat=False):
     """Get config as a dict."""
     settings = {
-        'nipype': nipype.get(),
+        'environment': environment.get(),
         'execution': execution.get(),
         'workflow': workflow.get(),
+        'nipype': nipype.get(),
     }
     if not flat:
         return settings
diff --git a/fmriprep/utils/sentry.py b/fmriprep/utils/sentry.py
index f7f406a48..12ba0ed58 100644
--- a/fmriprep/utils/sentry.py
+++ b/fmriprep/utils/sentry.py
@@ -43,7 +43,7 @@
 
 def sentry_setup():
     """Set-up sentry."""
-    release = config.execution.version or "dev"
+    release = config.environment.version or "dev"
     environment = "dev" if (
         os.getenv('FMRIPREP_DEV', '').lower in ('1', 'on', 'yes', 'y', 'true')
         or ('+' in release)
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 436f2706f..feeadde44 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -164,8 +164,8 @@ def init_single_subject_wf(subject_id):
 which is based on *Nipype* {nipype_ver}
 (@nipype1; @nipype2; RRID:SCR_002502).
 
-""".format(fmriprep_ver=config.execution.version,
-           nipype_ver=config.nipype.version)
+""".format(fmriprep_ver=config.environment.version,
+           nipype_ver=config.environment.nipype_version)
     workflow.__postdesc__ = """
 
 Many internal operations of *fMRIPrep* use
@@ -207,7 +207,7 @@ def init_single_subject_wf(subject_id):
                                      nstd_spaces=spaces.get_spaces(standard=False)),
                       name='summary', run_without_submitting=True)
 
-    about = pe.Node(AboutSummary(version=config.execution.version,
+    about = pe.Node(AboutSummary(version=config.environment.version,
                                  command=' '.join(sys.argv)),
                     name='about', run_without_submitting=True)
 

From 4d928481cd1c829a02d3b7c3b2ecf12fd882e895 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 13:08:10 -0800
Subject: [PATCH 21/43] fix: documentation build

---
 docs/workflows.rst                            |  90 ++----------------
 fmriprep/config.py                            |  11 ++-
 fmriprep/data/tests/config.toml               |  64 +++++++++++++
 fmriprep/data/tests/ds000005/CHANGES          |  12 +++
 fmriprep/data/tests/ds000005/README           |  22 +++++
 .../tests/ds000005/dataset_description.json   |   7 ++
 fmriprep/data/tests/ds000005/participants.tsv |  17 ++++
 .../ds000005/sub-01/anat/sub-01_T1w.nii.gz    | Bin 0 -> 96 bytes
 .../sub-01/anat/sub-01_inplaneT2.nii.gz       | Bin 0 -> 102 bytes
 ...1_task-mixedgamblestask_run-01_bold.nii.gz | Bin 0 -> 126 bytes
 ...01_task-mixedgamblestask_run-01_events.tsv |   0
 ...1_task-mixedgamblestask_run-02_bold.nii.gz | Bin 0 -> 126 bytes
 ...01_task-mixedgamblestask_run-02_events.tsv |   0
 ...1_task-mixedgamblestask_run-03_bold.nii.gz | Bin 0 -> 126 bytes
 ...01_task-mixedgamblestask_run-03_events.tsv |   0
 .../ds000005/task-mixedgamblestask_bold.json  |   4 +
 fmriprep/workflows/base.py                    |  14 +--
 fmriprep/workflows/bold/base.py               |   9 +-
 fmriprep/workflows/tests.py                   |  22 +++++
 19 files changed, 172 insertions(+), 100 deletions(-)
 create mode 100644 fmriprep/data/tests/config.toml
 create mode 100644 fmriprep/data/tests/ds000005/CHANGES
 create mode 100644 fmriprep/data/tests/ds000005/README
 create mode 100644 fmriprep/data/tests/ds000005/dataset_description.json
 create mode 100644 fmriprep/data/tests/ds000005/participants.tsv
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/anat/sub-01_T1w.nii.gz
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/anat/sub-01_inplaneT2.nii.gz
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_events.tsv
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_events.tsv
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
 create mode 100644 fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_events.tsv
 create mode 100644 fmriprep/data/tests/ds000005/task-mixedgamblestask_bold.json
 create mode 100644 fmriprep/workflows/tests.py

diff --git a/docs/workflows.rst b/docs/workflows.rst
index a42f4c71a..fec39bd9e 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -17,52 +17,10 @@ is presented below:
     :graph2use: orig
     :simple_form: yes
 
-    from collections import namedtuple
-    from niworkflows.utils.spaces import Reference, SpatialReferences
+    from fmriprep.workflows.tests import mock_config
     from fmriprep.workflows.base import init_single_subject_wf
-    BIDSLayout = namedtuple('BIDSLayout', ('root'))
-    wf = init_single_subject_wf(
-        anat_only=False,
-        aroma_melodic_dim=-200,
-        bold2t1w_dof=9,
-        cifti_output=False,
-        debug=False,
-        dummy_scans=None,
-        echo_idx=None,
-        err_on_aroma_warn=False,
-        fmap_bspline=False,
-        fmap_demean=True,
-        force_syn=True,
-        freesurfer=True,
-        hires=True,
-        ignore=[],
-        layout=BIDSLayout('.'),
-        longitudinal=False,
-        low_mem=False,
-        medial_surface_nan=False,
-        name='single_subject_wf',
-        omp_nthreads=1,
-        output_dir='.',
-        reportlets_dir='.',
-        regressors_all_comps=False,
-        regressors_dvars_th=1.5,
-        regressors_fd_th=0.5,
-        skull_strip_fixed_seed=False,
-        skull_strip_template=Reference('OASIS30ANTs'),
-        spaces=SpatialReferences(
-            spaces=[('MNI152Lin', {}),
-                    ('fsaverage', {'density': '10k'}),
-                    ('T1w', {}),
-                    ('fsnative', {})],
-            checkpoint=True),
-        subject_id='test',
-        t2s_coreg=False,
-        task_id='',
-        use_aroma=False,
-        use_bbr=True,
-        use_syn=True,
-        bids_filters=None,
-    )
+    mock_config()
+    wf = init_single_subject_wf()
 
 Preprocessing of structural MRI
 -------------------------------
@@ -279,44 +237,14 @@ BOLD preprocessing
     :graph2use: orig
     :simple_form: yes
 
+    from fmriprep.workflows.tests import mock_config
+    from fmriprep.workflows.bold.base import init_func_preproc_wf
+    mock_config()
+
     from collections import namedtuple
     from niworkflows.utils.spaces import SpatialReferences
-    from fmriprep.workflows.bold.base import init_func_preproc_wf
     BIDSLayout = namedtuple('BIDSLayout', ['root'])
-    wf = init_func_preproc_wf(
-        aroma_melodic_dim=-200,
-        bold2t1w_dof=9,
-        bold_file='/completely/made/up/path/sub-01_task-nback_bold.nii.gz',
-        cifti_output=False,
-        debug=False,
-        dummy_scans=None,
-        err_on_aroma_warn=False,
-        fmap_bspline=True,
-        fmap_demean=True,
-        force_syn=True,
-        freesurfer=True,
-        ignore=[],
-        low_mem=False,
-        medial_surface_nan=False,
-        omp_nthreads=1,
-        output_dir='.',
-        regressors_all_comps=False,
-        regressors_fd_th=0.5,
-        regressors_dvars_th=1.5,
-        reportlets_dir='.',
-        t2s_coreg=False,
-        spaces=SpatialReferences(
-            spaces=[('MNI152Lin', {}),
-                    ('fsaverage', {'density': '10k'}),
-                    ('T1w', {}),
-                    ('fsnative', {})],
-            checkpoint=True),
-        use_aroma=False,
-        use_bbr=True,
-        use_syn=True,
-        layout=BIDSLayout('.'),
-        num_bold=1,
-    )
+    wf = init_func_preproc_wf('sub-01_task-nback_bold.nii.gz')
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
 split into multiple sub-workflows described below.
@@ -396,7 +324,7 @@ Slice time correction
     wf = init_bold_stc_wf(
         metadata={'RepetitionTime': 2.0,
                   'SliceTiming': [0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9]},
-        )
+    )
 
 If the ``SliceTiming`` field is available within the input dataset metadata,
 this workflow performs slice time correction prior to other signal resampling
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 59d4f474f..9f3a547f7 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -499,7 +499,7 @@ def init_layout():
         execution._layout = BIDSLayout(
             str(execution.bids_dir),
             validate=False,
-            database_path=str(work_dir),
+            # database_path=str(work_dir),
             ignore=("code", "stimuli", "sourcedata", "models",
                     "derivatives", re.compile(r'^\.')))
     execution.layout = execution._layout
@@ -522,10 +522,13 @@ def set_logger_level():
 def init_spaces(checkpoint=True):
     """Get a spatial references."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
-    if getattr(workflow, 'spaces'):
+    if (
+        getattr(workflow, 'spaces')
+        and isinstance(workflow.spaces, SpatialReferences)
+    ):
         return
 
-    spaces = getattr(execution, 'output_spaces')
+    spaces = execution.output_spaces
     if spaces is not None and not isinstance(spaces, _SRs):
         spaces = SpatialReferences(
             [ref for s in execution.output_spaces.split(' ')
@@ -537,7 +540,7 @@ def init_spaces(checkpoint=True):
     if checkpoint:
         spaces.checkpoint()
 
-    internal = getattr(workflow, 'internal_spaces')
+    internal = workflow.internal_spaces
     if internal is not None and internal.strip():
         spaces += [ref for s in internal.split(' ')
                    for ref in Reference.from_string(s)]
diff --git a/fmriprep/data/tests/config.toml b/fmriprep/data/tests/config.toml
new file mode 100644
index 000000000..7179db39c
--- /dev/null
+++ b/fmriprep/data/tests/config.toml
@@ -0,0 +1,64 @@
+[environment]
+cpu_count = 8
+exec_env = "posix"
+free_mem = 2.2
+overcommit_policy = "heuristic"
+overcommit_limit = "50%"
+nipype_version = "1.5.0"
+templateflow_version = "0.4.2"
+version = "20.0.1"
+
+[execution]
+bids_dir = "ds000005/"
+bids_description_hash = "5d42e27751bbc884eca87cb4e62b9a0cca0cd86f8e578747fe89b77e6c5b21e5"
+boilerplate_only = false
+fs_license_file = "/opt/freesurfer/license.txt"
+fs_subjects_dir = "/opt/freesurfer/subjects"
+log_dir = "/home/oesteban/tmp/fmriprep-ds005/out/fmriprep/logs"
+log_level = 40
+low_mem = false
+md_only_boilerplate = false
+notrack = true
+output_dir = "/tmp"
+output_spaces = "MNI152NLin2009cAsym:res-2 MNI152NLin2009cAsym:res-native fsaverage:den-10k fsaverage:den-30k"
+reports_only = false
+run_uuid = "20200306-105302_d365772b-fd60-4741-a722-372c2f558b50"
+participant_label = [ "01",]
+templateflow_home = "~/.cache/templateflow"
+work_dir = "work/"
+write_graph = false
+
+[workflow]
+anat_only = false
+aroma_err_on_warn = false
+aroma_melodic_dim = -200
+bold2t1w_dof = 6
+fmap_bspline = false
+force_syn = false
+hires = true
+ignore = []
+internal_spaces = "fsaverage:den-164k MNI152NLin6Asym:res-2"
+longitudinal = false
+medial_surface_nan = false
+regressors_all_comps = false
+regressors_dvars_th = 1.5
+regressors_fd_th = 0.5
+run_reconall = true
+skull_strip_fixed_seed = false
+skull_strip_template = "OASIS30ANTs"
+t2s_coreg = false
+use_aroma = false
+
+[nipype]
+crashfile_format = "txt"
+get_linked_libs = false
+memory_gb = 32
+nprocs = 8
+omp_nthreads = 8
+plugin = "MultiProc"
+resource_monitor = false
+stop_on_first_crash = false
+
+[nipype.plugin_args]
+maxtasksperchild = 1
+raise_insufficient = false
diff --git a/fmriprep/data/tests/ds000005/CHANGES b/fmriprep/data/tests/ds000005/CHANGES
new file mode 100644
index 000000000..b5f26f448
--- /dev/null
+++ b/fmriprep/data/tests/ds000005/CHANGES
@@ -0,0 +1,12 @@
+2.0.1 2016-10-21
+  
+  - Added authors to dataset_discription.json
+
+1.0.1 2016-02-18
+
+  -  Update orientation information in nifti header for improved left-right determination
+
+
+1.0.0 2011-10-06
+
+  -  initial release
diff --git a/fmriprep/data/tests/ds000005/README b/fmriprep/data/tests/ds000005/README
new file mode 100644
index 000000000..fc6b833bd
--- /dev/null
+++ b/fmriprep/data/tests/ds000005/README
@@ -0,0 +1,22 @@
+This dataset was obtained from the OpenfMRI project (http://www.openfmri.org).
+Accession #: ds005
+Description: Mixed-gambles task
+
+Please cite the following references if you use these data:
+
+Tom, S.M., Fox, C.R., Trepel, C., Poldrack, R.A. (2007). The neural basis of loss aversion in decision-making under risk. Science, 315(5811):515-8
+
+
+Release history:
+10/06/2011: initial release
+3/21/2013: Updated release with QA information
+2/18/2016: Update orientation information in nifti header for improved left-right determination
+
+This dataset is made available under the Public Domain Dedication and License 
+v1.0, whose full text can be found at 
+http://www.opendatacommons.org/licenses/pddl/1.0/. 
+We hope that all users will follow the ODC Attribution/Share-Alike 
+Community Norms (http://www.opendatacommons.org/norms/odc-by-sa/); 
+in particular, while not legally required, we hope that all users 
+of the data will acknowledge the OpenfMRI project and NSF Grant 
+OCI-1131441 (R. Poldrack, PI) in any publications.
diff --git a/fmriprep/data/tests/ds000005/dataset_description.json b/fmriprep/data/tests/ds000005/dataset_description.json
new file mode 100644
index 000000000..1e7d03cbd
--- /dev/null
+++ b/fmriprep/data/tests/ds000005/dataset_description.json
@@ -0,0 +1,7 @@
+{
+    "BIDSVersion": "1.0.0rc4",
+    "License": "This dataset is made available under the Public Domain Dedication and License \nv1.0, whose full text can be found at \nhttp://www.opendatacommons.org/licenses/pddl/1.0/. \nWe hope that all users will follow the ODC Attribution/Share-Alike \nCommunity Norms (http://www.opendatacommons.org/norms/odc-by-sa/); \nin particular, while not legally required, we hope that all users \nof the data will acknowledge the OpenfMRI project and NSF Grant \nOCI-1131441 (R. Poldrack, PI) in any publications.",
+    "Name": "Mixed-gambles task",
+    "Authors": ["Tom, S.M.", "Fox, C.R.", "Trepel, C.", "Poldrack, R.A."],
+    "ReferencesAndLinks": "Tom, S.M., Fox, C.R., Trepel, C., Poldrack, R.A. (2007). The neural basis of loss aversion in decision-making under risk. Science, 315(5811):515-8"
+}
diff --git a/fmriprep/data/tests/ds000005/participants.tsv b/fmriprep/data/tests/ds000005/participants.tsv
new file mode 100644
index 000000000..48a1c9237
--- /dev/null
+++ b/fmriprep/data/tests/ds000005/participants.tsv
@@ -0,0 +1,17 @@
+participant_id	sex	age
+sub-01	M	28
+sub-02	F	21
+sub-03	F	27
+sub-04	M	25
+sub-05	F	20
+sub-06	M	20
+sub-07	F	24
+sub-08	M	25
+sub-09	F	19
+sub-10	M	20
+sub-11	M	20
+sub-12	M	21
+sub-13	F	22
+sub-14	F	19
+sub-15	F	20
+sub-16	M	22
diff --git a/fmriprep/data/tests/ds000005/sub-01/anat/sub-01_T1w.nii.gz b/fmriprep/data/tests/ds000005/sub-01/anat/sub-01_T1w.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..58f50bb603c9350e9d23e670c51d2e14ed34d66d
GIT binary patch
literal 96
zcmV-m0H6OKiwFn-xnf=d|8sR>Eif@(R55ohZfR)%i(zCS3NSOUfFUCT1fptkU~m8n
zG}tpR;KLi7A@ZoY2ad;t$7+y2&;hYx3=DbNhDe$}K+PJZA%QY-!T|t|_2nmE0{{SC
C?IU9V

literal 0
HcmV?d00001

diff --git a/fmriprep/data/tests/ds000005/sub-01/anat/sub-01_inplaneT2.nii.gz b/fmriprep/data/tests/ds000005/sub-01/anat/sub-01_inplaneT2.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..b35a0911446fee7170321b8e943e6d8dc931957c
GIT binary patch
literal 102
zcmV-s0Ga<EiwFn-xnf=d|8sR>Eif@(X>M?AVQytqGA?duX#k61WFQJKGq8XmBLf7Y
zYI0z301GtOGce%88=N8XsJaJ^$ArgfkU!7?v0@AidD@0Znm<6z8l@qDGIGKJ0FL$L
ICtw2r07;-F)Bpeg

literal 0
HcmV?d00001

diff --git a/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz b/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_bold.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..03fccb15f3d25b16f1103d7f673cc24644de076a
GIT binary patch
literal 126
zcmb2|=HOu5nH0zLzqm9>*T68oB(XSKH#f5)H6=YUHz_Bz7$gv1RGJ5pOv=wm(aX!s
zWav&zQQ$H#-q4_^%*?VVt0<v>f!pMUvB87G(sL9)t=Prhcf93z)&%<tj2n}9cq(tT
bdCanRI4iYOvC*jL5F<n1*Qe?U%nS?wUaBuH

literal 0
HcmV?d00001

diff --git a/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_events.tsv b/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-01_events.tsv
new file mode 100644
index 000000000..e69de29bb
diff --git a/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz b/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_bold.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..c329ab458628b8aa44770970475afb9c779cce08
GIT binary patch
literal 126
zcmb2|=HOu5nH0zLzqm9>*T68oB(XSKH#f5)H6=YUHz_Bz7$gv1RGO!2U=*K}pOd1O
zmzl}XotUD)WnjFaK~b5RWl>g9LIDG}$qi$J2ZyESD1KV8i@oo7%kiuU_7@m8Ch_o8
d-fHuhW$$oSYN=wQQPCkrhQ6;))f1Q*7yw@UFE0Q9

literal 0
HcmV?d00001

diff --git a/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_events.tsv b/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-02_events.tsv
new file mode 100644
index 000000000..e69de29bb
diff --git a/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz b/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_bold.nii.gz
new file mode 100644
index 0000000000000000000000000000000000000000..b46280f930c7d24c22507d6433c1867b22de45ed
GIT binary patch
literal 126
zcmb2|=HOu5nH0zLzqm9>*T68oB(XSKH#f5)H6=YUHz_Bz7$gv1RGO!2U>u*6pOd1O
zmzl}XotUD)WnjFaK~b5RWl>g9LIDG}$qi$J2ZyESD1KV8i@oo7%kiuU_7@m8Ch_o8
d-fHuhW$$oSYN=wQQPCkrhQ6;))f1Q*7yw^RFE9WA

literal 0
HcmV?d00001

diff --git a/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_events.tsv b/fmriprep/data/tests/ds000005/sub-01/func/sub-01_task-mixedgamblestask_run-03_events.tsv
new file mode 100644
index 000000000..e69de29bb
diff --git a/fmriprep/data/tests/ds000005/task-mixedgamblestask_bold.json b/fmriprep/data/tests/ds000005/task-mixedgamblestask_bold.json
new file mode 100644
index 000000000..e1e866658
--- /dev/null
+++ b/fmriprep/data/tests/ds000005/task-mixedgamblestask_bold.json
@@ -0,0 +1,4 @@
+{
+    "RepetitionTime": 2.0,
+    "TaskName": "mixed-gambles task"
+}
\ No newline at end of file
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index feeadde44..0f2c17918 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -46,13 +46,9 @@ def init_fmriprep_wf():
             :graph2use: orig
             :simple_form: yes
 
-            import os
-            from collections import namedtuple, OrderedDict
-            BIDSLayout = namedtuple('BIDSLayout', ['root'])
+            from fmriprep.workflows.tests import mock_config
             from fmriprep.workflows.base import init_fmriprep_wf
-            from niworkflows.utils.spaces import Reference, SpatialReferences
-
-            os.environ['FREESURFER_HOME'] = os.getcwd()
+            mock_config()
             wf = init_fmriprep_wf()
 
     """
@@ -111,11 +107,9 @@ def init_single_subject_wf(subject_id):
             :graph2use: orig
             :simple_form: yes
 
-            from collections import namedtuple
-            from niworkflows.utils.spaces import Reference, SpatialReferences
+            from fmriprep.workflows.tests import mock_config
             from fmriprep.workflows.base import init_single_subject_wf
-
-            BIDSLayout = namedtuple('BIDSLayout', ['root'])
+            mock_config()
             wf = init_single_subject_wf('test')
 
     Parameters
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index ab3b1f0b4..ef83347ed 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -50,11 +50,10 @@ def init_func_preproc_wf(bold_file):
             :graph2use: orig
             :simple_form: yes
 
-            from collections import namedtuple
-            from niworkflows.utils.spaces import SpatialReferences
-            from fmriprep.workflows.bold import init_func_preproc_wf
-            BIDSLayout = namedtuple('BIDSLayout', ['root'])
-            wf = init_func_preproc_wf()
+            from fmriprep.workflows.tests import mock_config
+            from fmriprep.workflows.bold.base import init_func_preproc_wf
+            mock_config()
+            wf = init_func_preproc_wf('sub-01_task-mixedgamblestask_run-01_bold.nii.gz')
 
     Parameters
     ----------
diff --git a/fmriprep/workflows/tests.py b/fmriprep/workflows/tests.py
new file mode 100644
index 000000000..67d71236c
--- /dev/null
+++ b/fmriprep/workflows/tests.py
@@ -0,0 +1,22 @@
+"""Utilities and mocks for testing and documentation building."""
+from pathlib import Path
+from pkg_resources import resource_filename as pkgrf
+from toml import loads
+from tempfile import mkdtemp
+
+
+def mock_config():
+    """Create a mock config for documentation and testing purposes."""
+    from .. import config
+    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
+    settings = loads(filename.read_text())
+    for sectionname, configs in settings.items():
+        if sectionname != 'environment':
+            section = getattr(config, sectionname)
+            section.load(configs)
+    config.set_logger_level()
+    config.init_spaces()
+
+    config.execution.work_dir = Path(mkdtemp())
+    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005'))
+    config.init_layout()

From 87c83ebb2ee506be016f3a88d78a6b34ddd273d2 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 13:59:47 -0800
Subject: [PATCH 22/43] fix: missing toml dep // sty: line too long

---
 fmriprep/cli/parser.py | 3 ++-
 setup.cfg              | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 5a1ca00a8..d8bb6e4e3 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -51,7 +51,8 @@ def _bids_filter(value):
     is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
 
     parser = ArgumentParser(
-        description='fMRIPrep: fMRI PREProcessing workflows v{}'.format(config.environment.version),
+        description='fMRIPrep: fMRI PREProcessing workflows v{}'.format(
+            config.environment.version),
         formatter_class=ArgumentDefaultsHelpFormatter)
     PathExists = partial(_path_exists, parser=parser)
     PositiveInt = partial(_min_one, parser=parser)
diff --git a/setup.cfg b/setup.cfg
index 40f2be6dd..433d609c7 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -33,6 +33,7 @@ install_requires =
     smriprep ~= 0.5.2
     tedana >= 0.0.5
     templateflow >= 0.4.2
+    toml
 test_requires =
     coverage
     codecov

From bd08c2adc1f96cf78a282f1f4fbb92c51db30e39 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 14:25:09 -0800
Subject: [PATCH 23/43] fix: add testing data to package data

---
 setup.cfg | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/setup.cfg b/setup.cfg
index 433d609c7..9baf2a6a4 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -79,6 +79,10 @@ fmriprep =
     data/itkIdentityTransform.txt
     data/flirtsch/bbr.sch
     data/reports-spec.yml
+    data/tests/config.toml
+    data/tests/ds000005/*
+    data/tests/ds000005/sub-01/anat/*
+    data/tests/ds000005/sub-01/func/*
     VERSION
 
 [options.entry_points]

From e7d7ac81dff8e055c7beed85e85a2af01f431156 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 16:41:14 -0800
Subject: [PATCH 24/43] fix(details): address various issues generating docs,
 running smoke tests, pytest, etc.

---
 docs/usage.rst                    |  2 +-
 docs/workflows.rst                | 21 ++++++++++----------
 fmriprep/cli/tests/test_parser.py |  2 +-
 fmriprep/config.py                | 33 ++++++++++++++++++-------------
 fmriprep/workflows/base.py        | 13 ++++++------
 fmriprep/workflows/bold/base.py   |  7 +++++--
 fmriprep/workflows/tests.py       | 14 ++++++++++++-
 7 files changed, 56 insertions(+), 36 deletions(-)

diff --git a/docs/usage.rst b/docs/usage.rst
index 0cd24ed78..7cb4d465b 100644
--- a/docs/usage.rst
+++ b/docs/usage.rst
@@ -31,7 +31,7 @@ Example: ::
 Command-Line Arguments
 ----------------------
 .. argparse::
-   :ref: fmriprep.cli.run.get_parser
+   :ref: fmriprep.cli.parser._build_parser
    :prog: fmriprep
    :nodefault:
    :nodefaultconst:
diff --git a/docs/workflows.rst b/docs/workflows.rst
index fec39bd9e..e14eb6a5f 100644
--- a/docs/workflows.rst
+++ b/docs/workflows.rst
@@ -19,8 +19,8 @@ is presented below:
 
     from fmriprep.workflows.tests import mock_config
     from fmriprep.workflows.base import init_single_subject_wf
-    mock_config()
-    wf = init_single_subject_wf()
+    with mock_config():
+        wf = init_single_subject_wf('01')
 
 Preprocessing of structural MRI
 -------------------------------
@@ -54,7 +54,7 @@ single reference template (see `Longitudinal processing`_).
         skull_strip_fixed_seed=False,
     )
 
-See also *sMRIPrep*'s 
+See also *sMRIPrep*'s
 :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`.
 
 .. _t1preproc_steps:
@@ -176,7 +176,7 @@ would be processed by the following command::
         -autorecon1 \
         -noskullstrip
 
-The second phase imports the brainmask calculated in the 
+The second phase imports the brainmask calculated in the
 `Preprocessing of structural MRI`_ sub-workflow.
 The final phase resumes reconstruction, using the T2w image to assist
 in finding the pial surface, if available.
@@ -238,13 +238,12 @@ BOLD preprocessing
     :simple_form: yes
 
     from fmriprep.workflows.tests import mock_config
+    from fmriprep import config
     from fmriprep.workflows.bold.base import init_func_preproc_wf
-    mock_config()
-
-    from collections import namedtuple
-    from niworkflows.utils.spaces import SpatialReferences
-    BIDSLayout = namedtuple('BIDSLayout', ['root'])
-    wf = init_func_preproc_wf('sub-01_task-nback_bold.nii.gz')
+    with mock_config():
+        bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
+            / 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+        wf = init_func_preproc_wf(str(bold_file))
 
 Preprocessing of :abbr:`BOLD (blood-oxygen level-dependent)` files is
 split into multiple sub-workflows described below.
@@ -429,7 +428,7 @@ Resampling BOLD runs onto standard spaces
 This sub-workflow concatenates the transforms calculated upstream (see
 `Head-motion estimation`_, `Susceptibility Distortion Correction (SDC)`_ --if
 fieldmaps are available--, `EPI to T1w registration`_, and an anatomical-to-standard
-transform from `Preprocessing of structural MRI`_) to map the 
+transform from `Preprocessing of structural MRI`_) to map the
 :abbr:`EPI (echo-planar imaging)`
 image to the standard spaces given by the ``--output-spaces`` argument
 (see :ref:`output-spaces`).
diff --git a/fmriprep/cli/tests/test_parser.py b/fmriprep/cli/tests/test_parser.py
index b9945d721..17dd3edfa 100644
--- a/fmriprep/cli/tests/test_parser.py
+++ b/fmriprep/cli/tests/test_parser.py
@@ -82,7 +82,7 @@ def test_get_parser_update(monkeypatch, capsys, current, latest):
     def _mock_check_latest(*args, **kwargs):
         return Version(latest)
 
-    monkeypatch.setattr(config.execution, 'version', current)
+    monkeypatch.setattr(config.environment, 'version', current)
     monkeypatch.setattr(_version, 'check_latest', _mock_check_latest)
 
     _build_parser()
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 9f3a547f7..de9d27475 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -7,22 +7,27 @@
 
 Example
 -------
->>> from fmriprep import config
->>> config_file = config.execution.work_dir / '.fmriprep.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
+
+.. code-block:: Python
+
+    >>> from fmriprep import config
+    >>> config_file = config.execution.work_dir / '.fmriprep.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
 
 The module also has a :py:func:`to_filename` function to allow writting out
-the settings to hard disk in *ToML* format, which looks like::
+the settings to hard disk in *ToML* format, which looks like
+
+.. code-block:: toml
 
     [environment]
     cpu_count = 8
diff --git a/fmriprep/workflows/base.py b/fmriprep/workflows/base.py
index 0f2c17918..c532d3a8b 100644
--- a/fmriprep/workflows/base.py
+++ b/fmriprep/workflows/base.py
@@ -48,8 +48,8 @@ def init_fmriprep_wf():
 
             from fmriprep.workflows.tests import mock_config
             from fmriprep.workflows.base import init_fmriprep_wf
-            mock_config()
-            wf = init_fmriprep_wf()
+            with mock_config():
+                wf = init_fmriprep_wf()
 
     """
     fmriprep_wf = Workflow(name='fmriprep_wf')
@@ -109,8 +109,8 @@ def init_single_subject_wf(subject_id):
 
             from fmriprep.workflows.tests import mock_config
             from fmriprep.workflows.base import init_single_subject_wf
-            mock_config()
-            wf = init_single_subject_wf('test')
+            with mock_config():
+                wf = init_single_subject_wf('01')
 
     Parameters
     ----------
@@ -222,15 +222,16 @@ def init_single_subject_wf(subject_id):
         freesurfer=config.workflow.run_reconall,
         hires=config.workflow.hires,
         longitudinal=config.workflow.longitudinal,
+        num_t1w=len(subject_data['t1w']),
         omp_nthreads=config.nipype.omp_nthreads,
         output_dir=str(config.execution.output_dir),
         reportlets_dir=reportlets_dir,
         skull_strip_fixed_seed=config.workflow.skull_strip_fixed_seed,
-        skull_strip_mode='force',
+        # skull_strip_mode='force',
         skull_strip_template=Reference.from_string(
             config.workflow.skull_strip_template)[0],
         spaces=spaces,
-        t1w=subject_data['t1w'],
+        # t1w=subject_data['t1w'],
     )
 
     workflow.connect([
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index ef83347ed..c9cb9b935 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -51,9 +51,12 @@ def init_func_preproc_wf(bold_file):
             :simple_form: yes
 
             from fmriprep.workflows.tests import mock_config
+            from fmriprep import config
             from fmriprep.workflows.bold.base import init_func_preproc_wf
-            mock_config()
-            wf = init_func_preproc_wf('sub-01_task-mixedgamblestask_run-01_bold.nii.gz')
+            with mock_config():
+                bold_file = config.execution.bids_dir / 'sub-01' / 'func' \
+                    / 'sub-01_task-mixedgamblestask_run-01_bold.nii.gz'
+                wf = init_func_preproc_wf(str(bold_file))
 
     Parameters
     ----------
diff --git a/fmriprep/workflows/tests.py b/fmriprep/workflows/tests.py
index 67d71236c..ed2fd66c2 100644
--- a/fmriprep/workflows/tests.py
+++ b/fmriprep/workflows/tests.py
@@ -1,13 +1,20 @@
 """Utilities and mocks for testing and documentation building."""
+import os
+from contextlib import contextmanager
 from pathlib import Path
 from pkg_resources import resource_filename as pkgrf
 from toml import loads
 from tempfile import mkdtemp
 
 
+@contextmanager
 def mock_config():
     """Create a mock config for documentation and testing purposes."""
     from .. import config
+    _old_fs = os.getenv('FREESURFER_HOME')
+    if not _old_fs:
+        os.environ['FREESURFER_HOME'] = mkdtemp()
+
     filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
     settings = loads(filename.read_text())
     for sectionname, configs in settings.items():
@@ -18,5 +25,10 @@ def mock_config():
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())
-    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005'))
+    config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005')).absolute()
     config.init_layout()
+
+    yield
+
+    if not _old_fs:
+        del os.environ["FREESURFER_HOME"]

From 3fb80ae25b6f0f0cddf93ebe12f797b3548b900f Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 20:11:48 -0800
Subject: [PATCH 25/43] fix: remove doctest, fix sloppy/debug flag

---
 docs/api.rst           |  5 +++++
 fmriprep/cli/parser.py |  2 +-
 fmriprep/config.py     | 28 ++++++++++++++--------------
 3 files changed, 20 insertions(+), 15 deletions(-)

diff --git a/docs/api.rst b/docs/api.rst
index 92e706171..adc61db18 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -4,6 +4,11 @@
 Developers - API
 ================
 
+Internal configuration system
+-----------------------------
+
+.. automodule:: fmriprep.config
+
 Workflows
 ---------
 
diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index d8bb6e4e3..c620855ad 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -278,7 +278,7 @@ def _bids_filter(value):
                               'the FMRIPREP developers. This information helps to '
                               'improve FMRIPREP and provides an indicator of real '
                               'world usage crucial for obtaining funding.')
-    g_other.add_argument('--sloppy', action='store_true', default=False,
+    g_other.add_argument('--sloppy', dest='debug', action='store_true', default=False,
                          help='Use low-quality tools for speed - TESTING ONLY')
 
     latest = check_latest()
diff --git a/fmriprep/config.py b/fmriprep/config.py
index de9d27475..0369c77a6 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -10,19 +10,19 @@
 
 .. code-block:: Python
 
-    >>> from fmriprep import config
-    >>> config_file = config.execution.work_dir / '.fmriprep.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
+    from fmriprep import config
+    config_file = config.execution.work_dir / '.fmriprep.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
 
 The module also has a :py:func:`to_filename` function to allow writting out
 the settings to hard disk in *ToML* format, which looks like
@@ -313,7 +313,7 @@ class execution(_Config):
     """A dictionary of BIDS selection filters."""
     boilerplate_only = False
     """Only generate a boilerplate."""
-    debug = None
+    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."""

From 3c732323dcd19fa347a2565df2293059e7383ace Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 23:00:42 -0800
Subject: [PATCH 26/43] fix: minor bugs remaining, derivatives check on circle

---
 .circleci/config.yml            | 8 ++++----
 fmriprep/config.py              | 5 +++--
 fmriprep/workflows/bold/base.py | 2 +-
 3 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index a710943c5..f4a0a3c29 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -414,7 +414,7 @@ jobs:
           name: Checking outputs of full fMRIPrep run
           command: |
             mkdir -p /tmp/ds005/test
-            find /tmp/ds005/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
+            find /tmp/ds005/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives/++ | sort > /tmp/ds005/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds005_outputs.txt /tmp/ds005/test/outputs.out
             exit $?
       - run:
@@ -437,7 +437,7 @@ jobs:
           command: |
             mkdir -p /tmp/ds005/test
             sudo rm -rf /tmp/ds005/derivatives_partial/freesurfer
-            find /tmp/ds005/derivatives_partial -path */figures -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
+            find /tmp/ds005/derivatives_partial \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds005/derivatives_partial/++ | sort > /tmp/ds005/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds005_partial_outputs.txt /tmp/ds005/test/outputs.out
             exit $?
       - run:
@@ -562,7 +562,7 @@ jobs:
           name: Checking outputs of fMRIPrep
           command: |
             mkdir -p /tmp/ds054/test
-            find /tmp/ds054/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
+            find /tmp/ds054/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds054/derivatives/++ | sort > /tmp/ds054/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds054_outputs.txt /tmp/ds054/test/outputs.out
             exit $?
       - run:
@@ -700,7 +700,7 @@ jobs:
           name: Checking outputs of fMRIPrep
           command: |
             mkdir -p /tmp/ds210/test
-            find /tmp/ds210/derivatives -path */figures -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
+            find /tmp/ds210/derivatives \( -path */figures -o -path */log \) -prune -o -name "*" -print | sed s+/tmp/ds210/derivatives/++ | sort > /tmp/ds210/test/outputs.out
             diff /tmp/src/fmriprep/.circleci/ds210_outputs.txt /tmp/ds210/test/outputs.out
             exit $?
       - run:
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 0369c77a6..c7ac9af9c 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -547,6 +547,7 @@ def init_spaces(checkpoint=True):
 
     internal = workflow.internal_spaces
     if internal is not None and internal.strip():
-        spaces += [ref for s in internal.split(' ')
-                   for ref in Reference.from_string(s)]
+        for ref in internal.split(' '):
+            spaces.add(ref)
+
     workflow.spaces = spaces
diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index c9cb9b935..92ca97d57 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -226,7 +226,7 @@ def init_func_preproc_wf(bold_file):
 
     # By default, force-bbr for t2s_coreg unless user specifies otherwise
     if config.workflow.t2s_coreg and config.workflow.use_bbr is None:
-        config.workflow.use_bbr.use_bbr = True
+        config.workflow.use_bbr = True
 
     # Build workflow
     workflow = Workflow(name=wf_name)

From 0b9760c2acb930cf944c7e081e90c021489ef8e6 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 6 Mar 2020 23:34:20 -0800
Subject: [PATCH 27/43] fix: remove flake8-putty, fix build_docs

---
 .travis.yml        |  2 +-
 fmriprep/config.py | 13 ++++++++-----
 setup.cfg          |  4 ----
 3 files changed, 9 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index adcc549ea..55f601d85 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -10,7 +10,7 @@ python:
 
 before_install:
   - python -m pip install --upgrade pip
-  - pip install "flake8<3.0" flake8-putty
+  - pip install flake8
 
 script:
   - flake8 fmriprep wrapper
diff --git a/fmriprep/config.py b/fmriprep/config.py
index c7ac9af9c..3e64ed4dd 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -545,9 +545,12 @@ def init_spaces(checkpoint=True):
     if checkpoint:
         spaces.checkpoint()
 
-    internal = workflow.internal_spaces
-    if internal is not None and internal.strip():
-        for ref in internal.split(' '):
-            spaces.add(ref)
-
+    if workflow.internal_spaces:
+        internal = [
+            Reference.from_string(ref)
+            for ref in workflow.internal_spaces.strip().split(' ')
+        ]
+        spaces += [
+            ref[0] for ref in internal if ref[0].fullname not in spaces
+        ]
     workflow.spaces = spaces
diff --git a/setup.cfg b/setup.cfg
index 9baf2a6a4..b2b3b022c 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -103,7 +103,3 @@ parentdir_prefix =
 max-line-length = 99
 doctests = True
 exclude=*build/
-putty-ignore =
-    */__init__.py : +F401
-    docs/conf.py : +E265
-    /^\s*\.\. _.*?: http/ : +E501

From fa6fe3a74a5cb4ce15844148ef09a6341e180bc1 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 7 Mar 2020 07:42:55 -0800
Subject: [PATCH 28/43] fix(ds210): failing for an unbound variable

---
 fmriprep/workflows/bold/base.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 92ca97d57..71d382e80 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -222,7 +222,7 @@ def init_func_preproc_wf(bold_file):
         config.loggers.workflow.warning(
             "No multiecho BOLD images found for T2* coregistration. "
             "Using standard EPI-T1 coregistration.")
-        t2s_coreg = False
+        config.workflow.t2s_coreg = False
 
     # By default, force-bbr for t2s_coreg unless user specifies otherwise
     if config.workflow.t2s_coreg and config.workflow.use_bbr is None:
@@ -410,7 +410,7 @@ def init_func_preproc_wf(bold_file):
         bold_t2s_wf = init_bold_t2s_wf(echo_times=tes,
                                        mem_gb=mem_gb['resampled'],
                                        omp_nthreads=omp_nthreads,
-                                       t2s_coreg=t2s_coreg,
+                                       t2s_coreg=config.workflow.t2s_coreg,
                                        name='bold_t2smap_wf')
 
         workflow.connect([

From 910295df1feb145df9892ea344da5bc647fa0305 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 7 Mar 2020 08:21:05 -0800
Subject: [PATCH 29/43] failed fix(ds005): ensure that spaces are being
 correctly read

it seems that the std_targets iterable of the workflow resampling ciftis
is not properly being filled in - apparently the spec is being dropped.

@mgxd - are there any changes in your side to niworkflows/spaces that
might have affected that particular?

The parameterized folders of nipype are like ``templatename.``, so it
seems the specs are not being honored.
---
 fmriprep/cli/run.py           | 25 ++++++++++++++-----------
 fmriprep/tests/__init__.py    |  0
 fmriprep/tests/test_config.py | 28 ++++++++++++++++++++++++++++
 3 files changed, 42 insertions(+), 11 deletions(-)
 create mode 100644 fmriprep/tests/__init__.py
 create mode 100644 fmriprep/tests/test_config.py

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index 4e1073a46..f6aa5434e 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -62,6 +62,17 @@ def main():
     # Clean up master process before running workflow, which may create forks
     gc.collect()
 
+    # Configure resource_monitor
+    if config.nipype.resource_monitor:
+        ncfg.update_config({
+            'monitoring': {
+                'enabled': config.nipype.resource_monitor,
+                'sample_frequency': '0.5',
+                'summary_append': True,
+            }
+        })
+        ncfg.enable_resource_monitor()
+
     # Nipype config (logs and execution)
     ncfg.update_config({
         'logging': {
@@ -70,20 +81,12 @@ def main():
         },
         'execution': {
             'crashdump_dir': str(config.execution.log_dir),
-            'crashfile_format': 'txt',
-            'get_linked_libs': False,
+            'crashfile_format': config.nipype.crashfile_format,
+            'get_linked_libs': config.nipype.get_linked_libs,
             'stop_on_first_crash': config.nipype.stop_on_first_crash,
-        },
-        'monitoring': {
-            'enabled': config.nipype.resource_monitor,
-            'sample_frequency': '0.5',
-            'summary_append': True,
         }
     })
 
-    if config.nipype.resource_monitor:
-        ncfg.enable_resource_monitor()
-
     # Sentry tracking
     if sentry_sdk is not None:
         with sentry_sdk.configure_scope() as scope:
@@ -92,10 +95,10 @@ def main():
         sentry_sdk.add_breadcrumb(message='fMRIPrep started', level='info')
         sentry_sdk.capture_message('fMRIPrep started', level='info')
 
-    config.loggers.workflow.log(25, 'fMRIPrep started!')
     config.loggers.workflow.log(15, '\n'.join(
         ['fMRIPrep config:'] + ['\t\t%s' % s for s in config.dumps().splitlines()])
     )
+    config.loggers.workflow.log(25, 'fMRIPrep started!')
     errno = 1  # Default is error exit unless otherwise set
     try:
         fmriprep_wf.run(**config.nipype.get_plugin())
diff --git a/fmriprep/tests/__init__.py b/fmriprep/tests/__init__.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/fmriprep/tests/test_config.py b/fmriprep/tests/test_config.py
new file mode 100644
index 000000000..04e19b894
--- /dev/null
+++ b/fmriprep/tests/test_config.py
@@ -0,0 +1,28 @@
+"""Check the configuration module and file."""
+from pathlib import Path
+from pkg_resources import resource_filename as pkgrf
+from toml import loads
+from niworkflows.utils.spaces import format_reference
+
+from .. import config
+
+
+def test_config_spaces():
+    """Check that all necessary spaces are recorded in the config."""
+    filename = Path(pkgrf('fmriprep', 'data/tests/config.toml'))
+    settings = loads(filename.read_text())
+    for sectionname, configs in settings.items():
+        if sectionname != 'environment':
+            section = getattr(config, sectionname)
+            section.load(configs)
+    config.set_logger_level()
+    config.init_spaces()
+
+    spaces = config.workflow.spaces
+    assert "MNI152NLin6Asym:res-2" in [
+        str(s) for s in spaces.get_standard(full_spec=True)]
+
+    assert "MNI152NLin6Asym_res-2" in [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references if s.standard and s.dim == 3
+    ]

From 3e7a791c00ca86030bbb892ee178e8006f6860ce Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 7 Mar 2020 18:01:04 -0800
Subject: [PATCH 30/43] fix(ds005): check whether cache needs a wipe

---
 .circleci/config.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index f4a0a3c29..f1118098c 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -334,10 +334,10 @@ jobs:
             - data-v7-{{ .Branch }}-{{ .Revision }}
       - restore_cache:
           keys:
-            - ds005-anat-v17-{{ .Branch }}-{{ .Revision }}
-            - ds005-anat-v17-{{ .Branch }}
-            - ds005-anat-v17-master
-            - ds005-anat-v17-
+            - ds005-anat-v18-{{ .Branch }}-{{ .Revision }}
+            - ds005-anat-v18-{{ .Branch }}
+            - ds005-anat-v18-master
+            - ds005-anat-v18-
       - run:
           name: Set-up a Docker registry
           command: |
@@ -380,7 +380,7 @@ jobs:
             rm -rf /tmp/ds005/work/reportlets
             rm -rf /tmp/ds005/derivatives/fmriprep
       - save_cache:
-         key: ds005-anat-v17-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
+         key: ds005-anat-v18-{{ .Branch }}-{{ .Revision }}-{{ epoch }}
          paths:
             - /tmp/ds005/work
 

From d51977ae10b6a5017bbe65b0deda20600ff47661 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 7 Mar 2020 19:02:43 -0800
Subject: [PATCH 31/43] enh(doc): better documentation of the config object

---
 docs/api.rst                  |   2 +-
 fmriprep/cli/parser.py        |   2 +-
 fmriprep/config.py            | 139 +++++++++++++++++++++++-----------
 fmriprep/tests/test_config.py |   2 +-
 fmriprep/workflows/tests.py   |   2 +-
 5 files changed, 99 insertions(+), 48 deletions(-)

diff --git a/docs/api.rst b/docs/api.rst
index adc61db18..88975e30f 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -3,11 +3,11 @@
 ================
 Developers - API
 ================
-
 Internal configuration system
 -----------------------------
 
 .. automodule:: fmriprep.config
+   :members: from_dict, load, get, dumps, to_filename, init_layout, init_spaces
 
 Workflows
 ---------
diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index c620855ad..a0f523eec 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -309,7 +309,7 @@ def parse_args(args=None, namespace=None):
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts))
 
-    config.set_logger_level()
+    config.init_loggers()
 
     # Retrieve logging level
     build_log = config.loggers.cli
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 3e64ed4dd..1ba3ab9bf 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -1,31 +1,15 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 r"""
-*fMRIPrep* settings.
+A Python module to maintain unique, run-wide *fMRIPrep* settings.
 
 This module implements the memory structures to keep a consistent, singleton config.
-
-Example
--------
-
-.. code-block:: Python
-
-    from fmriprep import config
-    config_file = config.execution.work_dir / '.fmriprep.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
-
-The module also has a :py:func:`to_filename` function to allow writting out
-the settings to hard disk in *ToML* format, which looks like
+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>/fmriprep.toml``.
+Settings are stored using :abbr:`ToML (Tom's Markup Language)`.
+The module has a :py:func:`~fmriprep.config.to_filename` function to allow writting out
+the settings to hard disk in *ToML* format, which looks like:
 
 .. code-block:: toml
 
@@ -90,14 +74,50 @@
     raise_insufficient = false
 
 This config file is used to pass the settings across processes,
-using the :py:func:`load` function.
+using the :py:func:`~fmriprep.config.load` function.
+
+Configuration sections
+----------------------
+.. autoclass:: environment
+   :members:
+.. autoclass:: execution
+   :members:
+.. autoclass:: workflow
+   :members:
+.. autoclass:: nipype
+   :members:
+
+Usage
+-----
+A config file is used to pass settings and collect information as the execution
+graph is built across processes.
+
+.. code-block:: Python
+
+    from fmriprep import config
+    config_file = config.execution.work_dir / '.fmriprep.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
+
+Other responsibilities
+----------------------
+Logging
+.......
 
-Other responsibilities of the config module:
+The :py:mod:`config` is responsible for other conveniency actions.
 
   * Switching Python's ``multiprocessing`` to *forkserver* mode.
-  * Set up new logger levels (25: IMPORTANT, and 15: VERBOSE).
-  * Set up a warnings filter as soon as possible.
-  * Initialize runtime descriptive settings (e.g., default FreeSurfer license,
+  * Set up a filter for warnings as early as possible.
+  * Initialize/crawl runtime descriptive settings (e.g., default FreeSurfer license,
     execution environment, nipype and *fMRIPrep* versions, etc.).
   * Automated I/O magic operations:
 
@@ -241,7 +261,16 @@ def get(cls):
 
 
 class environment(_Config):
-    """Read-only options."""
+    """
+    Read-only options regarding the platform and environment.
+
+    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 = os.cpu_count()
     """Number of available CPUs."""
@@ -264,7 +293,7 @@ class environment(_Config):
 
 
 class nipype(_Config):
-    """Nipype configuration."""
+    """Nipype settings."""
 
     crashfile_format = 'txt'
     """The file format for crashfiles, either text or pickle."""
@@ -303,10 +332,12 @@ def get_plugin(cls):
 
 
 class execution(_Config):
-    """Configure workflow-level settings."""
+    """Configure run-level settings."""
 
     bids_dir = None
-    """An existing path to the dataset, which must be BIDS-compliant."""
+    """An existing path to the dataset, which must be BIDS-compliant.
+    This config mutates to a :py:class:`~bids.layout.BIDSLayout` after calling
+    :py:func:`~fmriprep.config.init_layout`."""
     bids_description_hash = None
     """Checksum (SHA256) of the ``dataset_description.json`` of the BIDS dataset."""
     bids_filters = None
@@ -378,7 +409,7 @@ class execution(_Config):
 
 
 class workflow(_Config):
-    """Configure anatomical workflow."""
+    """Configure the particular execution graph of this workflow."""
 
     anat_only = False
     """Execute the anatomical preprocessing only."""
@@ -408,40 +439,60 @@ class workflow(_Config):
     longitudinal = False
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
     medial_surface_nan = None
-    """Fill medial surface with NaNs (not-a-number) when sampling."""
+    """Fill medial surface with :abbr:`NaNs (not-a-number)` when sampling."""
     regressors_all_comps = None
+    """Return all CompCor components."""
     regressors_dvars_th = None
+    """Threshold for DVARS."""
     regressors_fd_th = None
+    """Threshold for :abbr:`FD (frame-wise displacement)`."""
     run_reconall = True
     """Run FreeSurfer's surface reconstruction."""
     skull_strip_fixed_seed = False
     """Fix a seed for skull-stripping."""
-    skull_strip_template = 'OASIS30ANTs'
+    skull_strip_template = "OASIS30ANTs"
     """Change default brain extraction template."""
     spaces = None
     """Standard and nonstandard spaces."""
     t2s_coreg = None
-    r"""Co-register echos before generating the T2\* reference of ME-EPI."""
+    """Co-register echos before generating the T2\\* reference of \
+    :abbr:`ME-EPI (multi-echo echo-planar imaging)`."""
     use_aroma = None
     """Run ICA-AROMA."""
     use_bbr = None
     """Run boundary-based registration for BOLD-to-T1w registration (default: ``True``)."""
     use_syn = None
-    """Run *fieldmap-less* susceptibility-derived distortions estimation
+    """Run *fieldmap-less* susceptibility-derived distortions estimation \
     in the absence of any alternatives."""
 
 
 class loggers(_Config):
-    """Configure loggers."""
+    """
+    Setup loggers, providing access to them across the *fMRIPrep* run.
+
+        * Add new logger levels (25: IMPORTANT, and 15: VERBOSE).
+        * Add a new sub-logger (``cli``).
+        * Logger configuration.
+
+    See also:
+
+      .. autofunction: init_loggers
+
+    """
 
     _fmt = "%(asctime)s,%(msecs)d %(name)-2s " "%(levelname)-2s:\n\t %(message)s"
     _datefmt = "%y%m%d-%H:%M:%S"
 
     default = logging.getLogger()
+    """The root logger."""
     cli = logging.getLogger('cli')
+    """Command-line interface logging."""
     workflow = nlogging.getLogger('nipype.workflow')
+    """NiPype's workflow logger."""
     interface = nlogging.getLogger('nipype.interface')
+    """NiPype's interface logger."""
     utils = nlogging.getLogger('nipype.utils')
+    """NiPype's utils logger."""
 
 
 def from_dict(settings):
@@ -449,7 +500,7 @@ def from_dict(settings):
     nipype.load(settings)
     execution.load(settings)
     workflow.load(settings)
-    set_logger_level()
+    init_loggers()
 
 
 def load(filename):
@@ -461,7 +512,7 @@ def load(filename):
         if sectionname != 'environment':
             section = getattr(sys.modules[__name__], sectionname)
             section.load(configs)
-    set_logger_level()
+    init_loggers()
     init_spaces()
     init_layout()
 
@@ -495,7 +546,7 @@ def to_filename(filename):
 
 
 def init_layout():
-    """Init a new layout."""
+    """Create a new BIDS Layout on :attr:`~execution.bids_dir`."""
     if execution._layout is None:
         import re
         from bids.layout import BIDSLayout
@@ -510,8 +561,8 @@ def init_layout():
     execution.layout = execution._layout
 
 
-def set_logger_level():
-    """Set the current log level to all nipype loggers."""
+def init_loggers():
+    """Set the current log level to all loggers."""
     _handler = logging.StreamHandler(stream=sys.stdout)
     _handler.setFormatter(
         logging.Formatter(fmt=loggers._fmt, datefmt=loggers._datefmt)
@@ -525,7 +576,7 @@ def set_logger_level():
 
 
 def init_spaces(checkpoint=True):
-    """Get a spatial references."""
+    """Initialize the :attr:`~workflow.spaces` setting."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
     if (
         getattr(workflow, 'spaces')
diff --git a/fmriprep/tests/test_config.py b/fmriprep/tests/test_config.py
index 04e19b894..1da03fae6 100644
--- a/fmriprep/tests/test_config.py
+++ b/fmriprep/tests/test_config.py
@@ -15,7 +15,7 @@ def test_config_spaces():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
             section.load(configs)
-    config.set_logger_level()
+    config.init_loggers()
     config.init_spaces()
 
     spaces = config.workflow.spaces
diff --git a/fmriprep/workflows/tests.py b/fmriprep/workflows/tests.py
index ed2fd66c2..5ed955e77 100644
--- a/fmriprep/workflows/tests.py
+++ b/fmriprep/workflows/tests.py
@@ -21,7 +21,7 @@ def mock_config():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
             section.load(configs)
-    config.set_logger_level()
+    config.init_loggers()
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())

From 868b80c2025ffdf45a6549ae181626dc9bd94edb Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sat, 7 Mar 2020 22:54:41 -0800
Subject: [PATCH 32/43] fix: improve documentation and handle better artifacts
 in Circle

---
 .circleci/config.yml |  5 ++++-
 fmriprep/config.py   | 31 ++++++++++++++++---------------
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index f1118098c..b1fcbc1ba 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -166,6 +166,7 @@ jobs:
             printf "[execution]\nstop_on_first_crash = true\n" > /tmp/ds005/nipype.cfg
             echo "poll_sleep_duration = 0.01" >> /tmp/ds005/nipype.cfg
             echo "hash_method = content" >> /tmp/ds005/nipype.cfg
+            echo "crashfile_format = txt" >> /tmp/ds005/nipype.cfg
             cp /tmp/ds005/nipype.cfg /tmp/ds054/nipype.cfg
             cp /tmp/ds005/nipype.cfg /tmp/ds210/nipype.cfg
       - persist_to_workspace:
@@ -404,6 +405,8 @@ jobs:
                 --output-spaces MNI152NLin2009cAsym fsaverage5 fsnative MNI152NLin6Asym anat \
                 --use-plugin /home/circleci/src/fmriprep/.circleci/legacy.yml \
                 --nthreads 2 --cifti-output -vv
+      - store_artifacts:
+          path: /tmp/ds005/derivatives
       - run:
           name: Move intermediate results for second run
           command: |
@@ -458,7 +461,7 @@ jobs:
                 -exec sh -c 'rm -f {}; touch {}' \;
 
       - store_artifacts:
-          path: /tmp/ds005
+          path: /tmp/ds005/work
 
   ds054:
     machine:
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 1ba3ab9bf..1369a6e45 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -108,17 +108,17 @@
     # Access configs from any code section as:
     value = config.section.setting
 
-Other responsibilities
-----------------------
 Logging
-.......
+-------
+.. autoclass:: loggers
+   :members:
 
+Other responsibilities
+----------------------
 The :py:mod:`config` is responsible for other conveniency actions.
 
   * Switching Python's ``multiprocessing`` to *forkserver* mode.
   * Set up a filter for warnings as early as possible.
-  * Initialize/crawl runtime descriptive settings (e.g., default FreeSurfer license,
-    execution environment, nipype and *fMRIPrep* versions, etc.).
   * Automated I/O magic operations:
 
     * :obj:`Path` \<-\> :obj:`str` \<-\> :obj:`Path`).
@@ -264,6 +264,8 @@ class environment(_Config):
     """
     Read-only options regarding the platform and environment.
 
+    Crawls runtime descriptive settings (e.g., default FreeSurfer license,
+    execution environment, nipype and *fMRIPrep* 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,
@@ -335,9 +337,7 @@ class execution(_Config):
     """Configure run-level settings."""
 
     bids_dir = None
-    """An existing path to the dataset, which must be BIDS-compliant.
-    This config mutates to a :py:class:`~bids.layout.BIDSLayout` after calling
-    :py:func:`~fmriprep.config.init_layout`."""
+    """An existing path to the dataset, which must be BIDS-compliant."""
     bids_description_hash = None
     """Checksum (SHA256) of the ``dataset_description.json`` of the BIDS dataset."""
     bids_filters = None
@@ -353,7 +353,8 @@ class execution(_Config):
     fs_subjects_dir = None
     """FreeSurfer's subjects directory."""
     layout = None
-    """The path to the exported index of a py:class:`~bids.layout.BIDSLayout` object."""
+    """A py:class:`~bids.layout.BIDSLayout` object, see
+    :py:func:`~fmriprep.config.init_layout`."""
     log_dir = None
     """The path to a directory that contains execution logs."""
     log_level = 25
@@ -455,18 +456,18 @@ class workflow(_Config):
     spaces = None
     """Standard and nonstandard spaces."""
     t2s_coreg = None
-    """Co-register echos before generating the T2\\* reference of \
+    """Co-register echos before generating the T2\\* reference of
     :abbr:`ME-EPI (multi-echo echo-planar imaging)`."""
     use_aroma = None
-    """Run ICA-AROMA."""
+    """Run ICA-:abbr:`AROMA (automatic removal of motion artifacts)`."""
     use_bbr = None
-    """Run boundary-based registration for BOLD-to-T1w registration (default: ``True``)."""
+    """Run boundary-based registration for BOLD-to-T1w registration."""
     use_syn = None
-    """Run *fieldmap-less* susceptibility-derived distortions estimation \
+    """Run *fieldmap-less* susceptibility-derived distortions estimation
     in the absence of any alternatives."""
 
 
-class loggers(_Config):
+class loggers:
     """
     Setup loggers, providing access to them across the *fMRIPrep* run.
 
@@ -546,7 +547,7 @@ def to_filename(filename):
 
 
 def init_layout():
-    """Create a new BIDS Layout on :attr:`~execution.bids_dir`."""
+    """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
     if execution._layout is None:
         import re
         from bids.layout import BIDSLayout

From 8a0bf9d77dee8d557c92dd149e8eb7cc6a053a61 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Sun, 8 Mar 2020 22:43:59 -0700
Subject: [PATCH 33/43] fix: move Nipype and spaces to config module

---
 fmriprep/cli/parser.py          | 22 ---------
 fmriprep/cli/run.py             | 26 ----------
 fmriprep/config.py              | 88 ++++++++++++++++++++++++---------
 fmriprep/data/tests/config.toml |  1 -
 fmriprep/tests/test_config.py   | 12 +++++
 5 files changed, 78 insertions(+), 71 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index a0f523eec..f3c3128d6 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -403,25 +403,3 @@ def parse_args(args=None, namespace=None):
 
     config.execution.participant_label = sorted(participant_label)
     config.workflow.skull_strip_template = config.workflow.skull_strip_template[0]
-
-    # Ensure user-defined spatial references for outputs are correctly parsed.
-    # Certain options require normalization to a space not explicitly defined by users.
-    # These spaces will not be included in the final outputs.
-    internal_spaces = []
-    if config.workflow.use_aroma:
-        # Make sure there's a normalization to FSL for AROMA to use.
-        internal_spaces.append('MNI152NLin6Asym:res-2')
-
-    cifti_output = config.workflow.cifti_output
-    if cifti_output:
-        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
-        vol_res = '2' if cifti_output == '91k' else '1'
-        internal_spaces += ['fsaverage:den-164k', 'MNI152NLin6Asym:res-%s' % vol_res]
-
-    # These arguments implicitly signal expected output
-    spaces = config.execution.output_spaces
-    # Add the default standard space if not already present (required by several sub-workflows)
-    if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
-        internal_spaces.append("MNI152NLin2009cAsym")
-
-    config.workflow.internal_spaces = ' '.join(internal_spaces) or None
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index f6aa5434e..cfd33671a 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -9,7 +9,6 @@ def main():
     import os
     import sys
     import gc
-    from nipype import config as ncfg
     from multiprocessing import Process, Manager
     from .parser import parse_args
     from ..utils.bids import write_derivative_description
@@ -62,31 +61,6 @@ def main():
     # Clean up master process before running workflow, which may create forks
     gc.collect()
 
-    # Configure resource_monitor
-    if config.nipype.resource_monitor:
-        ncfg.update_config({
-            'monitoring': {
-                'enabled': config.nipype.resource_monitor,
-                'sample_frequency': '0.5',
-                'summary_append': True,
-            }
-        })
-        ncfg.enable_resource_monitor()
-
-    # Nipype config (logs and execution)
-    ncfg.update_config({
-        'logging': {
-            'log_directory': str(config.execution.log_dir),
-            'log_to_file': True
-        },
-        'execution': {
-            'crashdump_dir': str(config.execution.log_dir),
-            'crashfile_format': config.nipype.crashfile_format,
-            'get_linked_libs': config.nipype.get_linked_libs,
-            'stop_on_first_crash': config.nipype.stop_on_first_crash,
-        }
-    })
-
     # Sentry tracking
     if sentry_sdk is not None:
         with sentry_sdk.configure_scope() as scope:
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 1369a6e45..353def7d4 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -60,7 +60,6 @@
     force_syn = false
     hires = true
     ignore = []
-    internal_spaces = "MNI152NLin2009cAsym"
     longitudinal = false
     medial_surface_nan = false
     run_reconall = true
@@ -368,7 +367,8 @@ class execution(_Config):
     output_dir = None
     """Folder where derivatives will be stored."""
     output_spaces = None
-    """List of (non)standard spaces designated as spatial references for outputs."""
+    """List of (non)standard spaces designated (with the ``--output-spaces`` flag of
+    the command line) as spatial references for outputs."""
     reports_only = False
     """Only build the reports, based on the reportlets found in a cached working directory."""
     run_uuid = '%s_%s' % (strftime('%Y%m%d-%H%M%S'), uuid4())
@@ -435,8 +435,6 @@ class workflow(_Config):
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
     ignore = None
     """Ignore particular steps for *fMRIPrep*."""
-    internal_spaces = None
-    """Standard and nonstandard spaces."""
     longitudinal = False
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
     medial_surface_nan = None
@@ -454,7 +452,8 @@ class workflow(_Config):
     skull_strip_template = "OASIS30ANTs"
     """Change default brain extraction template."""
     spaces = None
-    """Standard and nonstandard spaces."""
+    """Keeps the :py:class:`~niworkflows.utils.spaces.SpatialReferences`
+    instance keeping standard and nonstandard spaces."""
     t2s_coreg = None
     """Co-register echos before generating the T2\\* reference of
     :abbr:`ME-EPI (multi-echo echo-planar imaging)`."""
@@ -513,6 +512,7 @@ def load(filename):
         if sectionname != 'environment':
             section = getattr(sys.modules[__name__], sectionname)
             section.load(configs)
+    init_nipype()
     init_loggers()
     init_spaces()
     init_layout()
@@ -564,6 +564,7 @@ def init_layout():
 
 def init_loggers():
     """Set the current log level to all loggers."""
+    from nipype import config as ncfg
     _handler = logging.StreamHandler(stream=sys.stdout)
     _handler.setFormatter(
         logging.Formatter(fmt=loggers._fmt, datefmt=loggers._datefmt)
@@ -574,35 +575,78 @@ def init_loggers():
     loggers.interface.setLevel(execution.log_level)
     loggers.workflow.setLevel(execution.log_level)
     loggers.utils.setLevel(execution.log_level)
+    ncfg.update_config({
+        'logging': {
+            'log_directory': str(execution.log_dir),
+            'log_to_file': True
+        },
+    })
 
 
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
-    if (
-        getattr(workflow, 'spaces')
-        and isinstance(workflow.spaces, SpatialReferences)
-    ):
-        return
-
     spaces = execution.output_spaces
-    if spaces is not None and not isinstance(spaces, _SRs):
+    if not isinstance(spaces, SpatialReferences):
         spaces = SpatialReferences(
             [ref for s in execution.output_spaces.split(' ')
              for ref in Reference.from_string(s)]
         )
-    if spaces is None:
-        spaces = _SRs()
+
+    # Add the default standard space if not already present (required by several sub-workflows)
+    if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
+        spaces.add(
+            Reference("MNI152NLin2009cAsym", {"res": "native"})
+        )
 
     if checkpoint:
         spaces.checkpoint()
 
-    if workflow.internal_spaces:
-        internal = [
-            Reference.from_string(ref)
-            for ref in workflow.internal_spaces.strip().split(' ')
-        ]
-        spaces += [
-            ref[0] for ref in internal if ref[0].fullname not in spaces
-        ]
+    # Ensure user-defined spatial references for outputs are correctly parsed.
+    # Certain options require normalization to a space not explicitly defined by users.
+    # These spaces will not be included in the final outputs.
+    if workflow.use_aroma:
+        # Make sure there's a normalization to FSL for AROMA to use.
+        spaces.add(
+            Reference("MNI152NLin6Asym", {"res": "2"})
+        )
+
+    cifti_output = workflow.cifti_output
+    if cifti_output:
+        # CIFTI grayordinates to corresponding FSL-MNI resolutions.
+        vol_res = '2' if cifti_output == '91k' else '1'
+        spaces.add(
+            Reference("fsaverage", {"den": "164k"})
+        )
+        spaces.add(
+            Reference("MNI152NLin6Asym", {"res": vol_res})
+        )
+
+    # Make the SpatialReferences object available
     workflow.spaces = spaces
+
+
+def init_nipype():
+    """Set NiPype configurations."""
+    from nipype import config as ncfg
+
+    # Configure resource_monitor
+    if nipype.resource_monitor:
+        ncfg.update_config({
+            'monitoring': {
+                'enabled': nipype.resource_monitor,
+                'sample_frequency': '0.5',
+                'summary_append': True,
+            }
+        })
+        ncfg.enable_resource_monitor()
+
+    # Nipype config (logs and execution)
+    ncfg.update_config({
+        'execution': {
+            'crashdump_dir': str(execution.log_dir),
+            'crashfile_format': nipype.crashfile_format,
+            'get_linked_libs': nipype.get_linked_libs,
+            'stop_on_first_crash': nipype.stop_on_first_crash,
+        }
+    })
diff --git a/fmriprep/data/tests/config.toml b/fmriprep/data/tests/config.toml
index 7179db39c..d02b31f38 100644
--- a/fmriprep/data/tests/config.toml
+++ b/fmriprep/data/tests/config.toml
@@ -37,7 +37,6 @@ fmap_bspline = false
 force_syn = false
 hires = true
 ignore = []
-internal_spaces = "fsaverage:den-164k MNI152NLin6Asym:res-2"
 longitudinal = false
 medial_surface_nan = false
 regressors_all_comps = false
diff --git a/fmriprep/tests/test_config.py b/fmriprep/tests/test_config.py
index 1da03fae6..f3ed7c8b0 100644
--- a/fmriprep/tests/test_config.py
+++ b/fmriprep/tests/test_config.py
@@ -19,6 +19,18 @@ def test_config_spaces():
     config.init_spaces()
 
     spaces = config.workflow.spaces
+    assert "MNI152NLin6Asym:res-2" not in [
+        str(s) for s in spaces.get_standard(full_spec=True)]
+
+    assert "MNI152NLin6Asym_res-2" not in [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references if s.standard and s.dim == 3
+    ]
+
+    config.workflow.use_aroma = True
+    config.init_spaces()
+    spaces = config.workflow.spaces
+
     assert "MNI152NLin6Asym:res-2" in [
         str(s) for s in spaces.get_standard(full_spec=True)]
 

From a0cdd845d5e310543b374d636a69b6999fcdff29 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 10:19:10 -0700
Subject: [PATCH 34/43] Apply suggestions from code review

Co-Authored-By: Mathias Goncalves <goncalves.mathias@gmail.com>
---
 fmriprep/cli/parser.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index f3c3128d6..23bd7fcde 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -21,7 +21,7 @@ def _build_parser():
     def _path_exists(path, parser):
         """Ensure a given path exists."""
         if path is None or not Path(path).exists():
-            raise parser.error("Path does not exist: <%s>." % path)
+            raise parser.error(f"Path does not exist: <{path}>.")
         return Path(path).absolute()
 
     def _min_one(value, parser):
@@ -46,7 +46,7 @@ def _bids_filter(value):
         if value and Path(value).exists():
             return loads(Path(value).read_text())
 
-    verstr = 'fMRIPrep v{}'.format(config.environment.version)
+    verstr = f'fMRIPrep v{config.environment.version}'
     currentv = Version(config.environment.version)
     is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
 
@@ -360,14 +360,14 @@ def parse_args(args=None, namespace=None):
 
     # Ensure input and output folders are not the same
     if output_dir == bids_dir:
-        config.loggers.cli.error(
+        parser.error(
             'The selected output folder is the same as the input BIDS folder. '
             'Please modify the output path (suggestion: %s).'
             % bids_dir / 'derivatives' / ('fmriprep-%s' % version.split('+')[0])
         )
 
     if bids_dir in work_dir.parents:
-        config.loggers.cli.error(
+        parser.error(
             'The selected working directory is a subdirectory of the input BIDS folder. '
             'Please modify the output path.'
         )

From e81839fbeabec6d0ade8f5807319743e749dc997 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 12:00:50 -0700
Subject: [PATCH 35/43] enh: make some init methods classmethods

---
 docs/api.rst                  |   2 +-
 fmriprep/cli/parser.py        |   7 +-
 fmriprep/cli/workflow.py      |   1 -
 fmriprep/config.py            | 174 ++++++++++++++++------------------
 fmriprep/tests/test_config.py |   5 +-
 fmriprep/workflows/tests.py   |   7 +-
 6 files changed, 95 insertions(+), 101 deletions(-)

diff --git a/docs/api.rst b/docs/api.rst
index 88975e30f..0eee5518a 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -7,7 +7,7 @@ Internal configuration system
 -----------------------------
 
 .. automodule:: fmriprep.config
-   :members: from_dict, load, get, dumps, to_filename, init_layout, init_spaces
+   :members: from_dict, load, get, dumps, to_filename, init_spaces
 
 Workflows
 ---------
diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 23bd7fcde..0e4a844f0 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -308,8 +308,7 @@ def parse_args(args=None, namespace=None):
     opts = parser.parse_args(args, namespace)
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts))
-
-    config.init_loggers()
+    config.loggers.init()
 
     # Retrieve logging level
     build_log = config.loggers.cli
@@ -388,8 +387,8 @@ def parse_args(args=None, namespace=None):
     output_dir.mkdir(exist_ok=True, parents=True)
     work_dir.mkdir(exist_ok=True, parents=True)
 
-    # First check that bids_dir looks like a BIDS folder
-    config.init_layout()
+    # Force initialization of the BIDSLayout
+    config.execution.init()
     all_subjects = config.execution.layout.get_subjects()
     if config.execution.participant_label is None:
         config.execution.participant_label = all_subjects
diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
index af2bbf120..6a3ddc55c 100644
--- a/fmriprep/cli/workflow.py
+++ b/fmriprep/cli/workflow.py
@@ -42,7 +42,6 @@ def build_workflow(config_file, retval):
         config.execution.bids_description_hash = sha256(desc_content).hexdigest()
 
     # First check that bids_dir looks like a BIDS folder
-    config.init_layout()
     subject_list = collect_participants(
         config.execution.layout,
         participant_label=config.execution.participant_label
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 353def7d4..dd2b44ed9 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -116,15 +116,11 @@
 ----------------------
 The :py:mod:`config` is responsible for other conveniency actions.
 
-  * Switching Python's ``multiprocessing`` to *forkserver* mode.
+  * Switching Python's :obj:`multiprocessing` to *forkserver* mode.
   * Set up a filter for warnings as early as possible.
-  * Automated I/O magic operations:
-
-    * :obj:`Path` \<-\> :obj:`str` \<-\> :obj:`Path`).
-    * :py:class:`~niworkflows.util.spaces.SpatialReferences` \<-\> :obj:`str` \<-\>
-      :py:class:`~niworkflows.util.spaces.SpatialReferences`
-    * :py:class:`~bids.layout.BIDSLayout` \<-\> :obj:`str` \<-\>
-      :py:class:`~bids.layout.BIDSLayout`
+  * Automated I/O magic operations. Some conversions need to happen in the
+    store/load processes (e.g., from/to :obj:`~pathlib.Path` \<-\> :obj:`str`,
+    :py:class:`~bids.layout.BIDSLayout`, etc.)
 
 """
 from multiprocessing import set_start_method
@@ -229,7 +225,7 @@ def __init__(self):
         raise RuntimeError('Configuration type is not instantiable.')
 
     @classmethod
-    def load(cls, settings):
+    def load(cls, settings, init=True):
         """Store settings from a dictionary."""
         for k, v in settings.items():
             if v is None:
@@ -240,6 +236,12 @@ def load(cls, settings):
             if hasattr(cls, k):
                 setattr(cls, k, v)
 
+        if init:
+            try:
+                cls.init()
+            except AttributeError:
+                pass
+
     @classmethod
     def get(cls):
         """Return defined settings."""
@@ -331,6 +333,32 @@ def get_plugin(cls):
                 out['plugin_args']['memory_gb'] = float(cls.memory_gb)
         return out
 
+    @classmethod
+    def init(cls):
+        """Set NiPype configurations."""
+        from nipype import config as ncfg
+
+        # Configure resource_monitor
+        if cls.resource_monitor:
+            ncfg.update_config({
+                'monitoring': {
+                    'enabled': cls.resource_monitor,
+                    'sample_frequency': '0.5',
+                    'summary_append': True,
+                }
+            })
+            ncfg.enable_resource_monitor()
+
+        # Nipype config (logs and execution)
+        ncfg.update_config({
+            'execution': {
+                'crashdump_dir': str(execution.log_dir),
+                'crashfile_format': cls.crashfile_format,
+                'get_linked_libs': cls.get_linked_libs,
+                'stop_on_first_crash': cls.stop_on_first_crash,
+            }
+        })
+
 
 class execution(_Config):
     """Configure run-level settings."""
@@ -352,8 +380,7 @@ class execution(_Config):
     fs_subjects_dir = None
     """FreeSurfer's subjects directory."""
     layout = None
-    """A py:class:`~bids.layout.BIDSLayout` object, see
-    :py:func:`~fmriprep.config.init_layout`."""
+    """A :py:class:`~bids.layout.BIDSLayout` object, see :py:func:`init`."""
     log_dir = None
     """The path to a directory that contains execution logs."""
     log_level = 25
@@ -397,6 +424,22 @@ class execution(_Config):
         'work_dir',
     )
 
+    @classmethod
+    def init(cls):
+        """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
+        if cls._layout is None:
+            import re
+            from bids.layout import BIDSLayout
+            work_dir = cls.work_dir / 'bids.db'
+            work_dir.mkdir(exist_ok=True, parents=True)
+            cls._layout = BIDSLayout(
+                str(cls.bids_dir),
+                validate=False,
+                # database_path=str(work_dir),
+                ignore=("code", "stimuli", "sourcedata", "models",
+                        "derivatives", re.compile(r'^\.')))
+        cls.layout = cls._layout
+
 
 # These variables are not necessary anymore
 del _fs_license
@@ -467,18 +510,7 @@ class workflow(_Config):
 
 
 class loggers:
-    """
-    Setup loggers, providing access to them across the *fMRIPrep* run.
-
-        * Add new logger levels (25: IMPORTANT, and 15: VERBOSE).
-        * Add a new sub-logger (``cli``).
-        * Logger configuration.
-
-    See also:
-
-      .. autofunction: init_loggers
-
-    """
+    """Keep loggers easily accessible (see :py:func:`init`)."""
 
     _fmt = "%(asctime)s,%(msecs)d %(name)-2s " "%(levelname)-2s:\n\t %(message)s"
     _datefmt = "%y%m%d-%H:%M:%S"
@@ -494,13 +526,41 @@ class loggers:
     utils = nlogging.getLogger('nipype.utils')
     """NiPype's utils logger."""
 
+    @classmethod
+    def init(cls):
+        """
+        Set the log level, initialize all loggers into :py:class:`loggers`.
+
+            * Add new logger levels (25: IMPORTANT, and 15: VERBOSE).
+            * Add a new sub-logger (``cli``).
+            * Logger configuration.
+
+        """
+        from nipype import config as ncfg
+        _handler = logging.StreamHandler(stream=sys.stdout)
+        _handler.setFormatter(
+            logging.Formatter(fmt=cls._fmt, datefmt=cls._datefmt)
+        )
+        cls.cli.addHandler(_handler)
+        cls.default.setLevel(execution.log_level)
+        cls.cli.setLevel(execution.log_level)
+        cls.interface.setLevel(execution.log_level)
+        cls.workflow.setLevel(execution.log_level)
+        cls.utils.setLevel(execution.log_level)
+        ncfg.update_config({
+            'logging': {
+                'log_directory': str(execution.log_dir),
+                'log_to_file': True
+            },
+        })
+
 
 def from_dict(settings):
     """Read settings from a flat dictionary."""
     nipype.load(settings)
     execution.load(settings)
     workflow.load(settings)
-    init_loggers()
+    loggers.init()
 
 
 def load(filename):
@@ -512,10 +572,7 @@ def load(filename):
         if sectionname != 'environment':
             section = getattr(sys.modules[__name__], sectionname)
             section.load(configs)
-    init_nipype()
-    init_loggers()
     init_spaces()
-    init_layout()
 
 
 def get(flat=False):
@@ -546,43 +603,6 @@ def to_filename(filename):
     filename.write_text(dumps())
 
 
-def init_layout():
-    """Create a new BIDS Layout accessible with :attr:`~execution.layout`."""
-    if execution._layout is None:
-        import re
-        from bids.layout import BIDSLayout
-        work_dir = execution.work_dir / 'bids.db'
-        work_dir.mkdir(exist_ok=True, parents=True)
-        execution._layout = BIDSLayout(
-            str(execution.bids_dir),
-            validate=False,
-            # database_path=str(work_dir),
-            ignore=("code", "stimuli", "sourcedata", "models",
-                    "derivatives", re.compile(r'^\.')))
-    execution.layout = execution._layout
-
-
-def init_loggers():
-    """Set the current log level to all loggers."""
-    from nipype import config as ncfg
-    _handler = logging.StreamHandler(stream=sys.stdout)
-    _handler.setFormatter(
-        logging.Formatter(fmt=loggers._fmt, datefmt=loggers._datefmt)
-    )
-    loggers.cli.addHandler(_handler)
-    loggers.default.setLevel(execution.log_level)
-    loggers.cli.setLevel(execution.log_level)
-    loggers.interface.setLevel(execution.log_level)
-    loggers.workflow.setLevel(execution.log_level)
-    loggers.utils.setLevel(execution.log_level)
-    ncfg.update_config({
-        'logging': {
-            'log_directory': str(execution.log_dir),
-            'log_to_file': True
-        },
-    })
-
-
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
@@ -624,29 +644,3 @@ def init_spaces(checkpoint=True):
 
     # Make the SpatialReferences object available
     workflow.spaces = spaces
-
-
-def init_nipype():
-    """Set NiPype configurations."""
-    from nipype import config as ncfg
-
-    # Configure resource_monitor
-    if nipype.resource_monitor:
-        ncfg.update_config({
-            'monitoring': {
-                'enabled': nipype.resource_monitor,
-                'sample_frequency': '0.5',
-                'summary_append': True,
-            }
-        })
-        ncfg.enable_resource_monitor()
-
-    # Nipype config (logs and execution)
-    ncfg.update_config({
-        'execution': {
-            'crashdump_dir': str(execution.log_dir),
-            'crashfile_format': nipype.crashfile_format,
-            'get_linked_libs': nipype.get_linked_libs,
-            'stop_on_first_crash': nipype.stop_on_first_crash,
-        }
-    })
diff --git a/fmriprep/tests/test_config.py b/fmriprep/tests/test_config.py
index f3ed7c8b0..c43513657 100644
--- a/fmriprep/tests/test_config.py
+++ b/fmriprep/tests/test_config.py
@@ -14,8 +14,9 @@ def test_config_spaces():
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
-            section.load(configs)
-    config.init_loggers()
+            section.load(configs, init=False)
+    config.nipype.init()
+    config.loggers.init()
     config.init_spaces()
 
     spaces = config.workflow.spaces
diff --git a/fmriprep/workflows/tests.py b/fmriprep/workflows/tests.py
index 5ed955e77..d34c8db13 100644
--- a/fmriprep/workflows/tests.py
+++ b/fmriprep/workflows/tests.py
@@ -20,13 +20,14 @@ def mock_config():
     for sectionname, configs in settings.items():
         if sectionname != 'environment':
             section = getattr(config, sectionname)
-            section.load(configs)
-    config.init_loggers()
+            section.load(configs, init=False)
+    config.nipype.init()
+    config.loggers.init()
     config.init_spaces()
 
     config.execution.work_dir = Path(mkdtemp())
     config.execution.bids_dir = Path(pkgrf('fmriprep', 'data/tests/ds000005')).absolute()
-    config.init_layout()
+    config.execution.init()
 
     yield
 

From 3e3bb9053ca0395201954bdcebfbe4c71ef01ff4 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 12:28:31 -0700
Subject: [PATCH 36/43] docs: import config file from package data

---
 fmriprep/config.py | 65 ++++------------------------------------------
 1 file changed, 5 insertions(+), 60 deletions(-)

diff --git a/fmriprep/config.py b/fmriprep/config.py
index dd2b44ed9..3b3114b5d 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -11,66 +11,10 @@
 The module has a :py:func:`~fmriprep.config.to_filename` function to allow writting out
 the settings to hard disk in *ToML* format, which looks like:
 
-.. code-block:: toml
-
-    [environment]
-    cpu_count = 8
-    exec_env = "posix"
-    free_mem = 2.2
-    overcommit_policy = "heuristic"
-    overcommit_limit = "50%"
-    nipype_version = "1.5.0"
-    templateflow_version = "0.4.2"
-    version = "20.0.1"
-
-    [nipype]
-    crashfile_format = "txt"
-    get_linked_libs = false
-    nprocs = 8
-    omp_nthreads = 8
-    plugin = "MultiProc"
-    resource_monitor = false
-    stop_on_first_crash = false
-
-    [execution]
-    bids_dir = "/data/openfmri/ds000005"
-    boilerplate_only = false
-    exec_env = "posix"
-    fs_license_file = "/opt/freesurfer/license.txt"
-    fs_subjects_dir = "/data/openfmri/ds000005/derivatives/freesurfer-6.0.1"
-    log_dir = "/data/openfmri/ds000005/derivatives/fmriprep/logs"
-    log_level = 15
-    low_mem = false
-    md_only_boilerplate = false
-    notrack = true
-    output_dir = "/data/openfmri/ds000005/derivatives"
-    reports_only = false
-    run_uuid = "20200302-174345_9ba9f304-82de-4538-8c3a-570c5f5d8f2f"
-    participant_label = [ "01",]
-    work_dir = "work/"
-    write_graph = false
-
-    [workflow]
-    anat_only = false
-    aroma_err_on_warn = false
-    aroma_melodic_dim = -200
-    bold2t1w_dof = 6
-    cifti_output = false
-    fmap_bspline = false
-    force_syn = false
-    hires = true
-    ignore = []
-    longitudinal = false
-    medial_surface_nan = false
-    run_reconall = true
-    skull_strip_fixed_seed = false
-    skull_strip_template = "OASIS30ANTs"
-    t2s_coreg = false
-    use_aroma = false
-
-    [nipype.plugin_args]
-    maxtasksperchild = 1
-    raise_insufficient = false
+.. literalinclude:: ../fmriprep/data/tests/config.toml
+   :language: toml
+   :name: fmriprep.toml
+   :caption: **Example file representation of fMRIPrep settings**.
 
 This config file is used to pass the settings across processes,
 using the :py:func:`~fmriprep.config.load` function.
@@ -129,6 +73,7 @@
 # cmp is not used by fmriprep, so ignore nipype-generated warnings
 warnings.filterwarnings('ignore', 'cmp not installed')
 warnings.filterwarnings('ignore', 'This has not been fully tested. Please report any failures.')
+warnings.filterwarnings('ignore', "sklearn.externals.joblib is deprecated in 0.21")
 warnings.filterwarnings('ignore', "can't resolve package from __spec__ or __package__")
 warnings.filterwarnings('ignore', category=DeprecationWarning)
 warnings.filterwarnings('ignore', category=FutureWarning)

From 8dc07e20c76e7ca10545be4f946ab293766e1484 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 22:59:49 -0700
Subject: [PATCH 37/43] Update fmriprep/cli/parser.py [skip ci]

Co-Authored-By: Mathias Goncalves <goncalves.mathias@gmail.com>
---
 fmriprep/cli/parser.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 0e4a844f0..765a63815 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -396,7 +396,7 @@ def parse_args(args=None, namespace=None):
     participant_label = set(config.execution.participant_label)
     missing_subjects = participant_label - set(all_subjects)
     if missing_subjects:
-        config.loggers.cli.error(
+        parser.error(
             "One or more participant labels were not found in the BIDS directory: "
             "%s." % ", ".join(missing_subjects))
 

From 881993ede4249ad0ac2c85b8238043214fadbaf5 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 22:58:16 -0700
Subject: [PATCH 38/43] fix: bug identified by @mgxd on edge
 ``--output-spaces`` cases

---
 fmriprep/cli/parser.py        | 13 ++++++++++---
 fmriprep/config.py            | 12 ++++++------
 fmriprep/tests/test_config.py | 12 ++++++++++++
 3 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 765a63815..c66af6b03 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -142,7 +142,7 @@ def _bids_filter(value):
              'option is not enabled, standard EPI-T1 coregistration is performed '
              'using the middle echo.')
     g_conf.add_argument(
-        '--output-spaces', nargs='+', action=OutputReferencesAction, default=SpatialReferences(),
+        '--output-spaces', nargs='*', action=OutputReferencesAction,
         help="""\
 Standard and non-standard spaces to resample anatomical and functional images to. \
 Standard spaces may be specified by the form \
@@ -151,8 +151,8 @@ def _bids_filter(value):
 colon-separated parameters. \
 Non-standard spaces imply specific orientations and sampling grids. \
 Important to note, the ``res-*`` modifier does not define the resolution used for \
-the spatial normalization.
-For further details, please check out \
+the spatial normalization. To generate no BOLD outputs, use this option without specifying \
+any spatial references. For further details, please check out \
 https://fmriprep.readthedocs.io/en/%s/spaces.html""" % (currentv.base_version
                                                         if is_release else 'latest'))
 
@@ -304,12 +304,19 @@ def _bids_filter(value):
 def parse_args(args=None, namespace=None):
     """Parse args and run further checks on the command line."""
     import logging
+    from niworkflows.utils.spaces import Reference, SpatialReferences
     parser = _build_parser()
     opts = parser.parse_args(args, namespace)
     config.execution.log_level = int(max(25 - 5 * opts.verbose_count, logging.DEBUG))
     config.from_dict(vars(opts))
     config.loggers.init()
 
+    # Initialize --output-spaces if not defined
+    if config.execution.output_spaces is None:
+        config.execution.output_spaces = SpatialReferences(
+            [Reference("MNI152NLin2009cAsym", {"res": "native"})]
+        )
+
     # Retrieve logging level
     build_log = config.loggers.cli
 
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 3b3114b5d..67428b0ee 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -551,22 +551,22 @@ def to_filename(filename):
 def init_spaces(checkpoint=True):
     """Initialize the :attr:`~workflow.spaces` setting."""
     from niworkflows.utils.spaces import Reference, SpatialReferences
-    spaces = execution.output_spaces
+    spaces = execution.output_spaces or SpatialReferences()
     if not isinstance(spaces, SpatialReferences):
         spaces = SpatialReferences(
-            [ref for s in execution.output_spaces.split(' ')
+            [ref for s in spaces.split(' ')
              for ref in Reference.from_string(s)]
         )
 
+    if checkpoint and not spaces.is_cached():
+        spaces.checkpoint()
+
     # Add the default standard space if not already present (required by several sub-workflows)
     if "MNI152NLin2009cAsym" not in spaces.get_spaces(nonstandard=False, dim=(3,)):
         spaces.add(
-            Reference("MNI152NLin2009cAsym", {"res": "native"})
+            Reference("MNI152NLin2009cAsym", {})
         )
 
-    if checkpoint:
-        spaces.checkpoint()
-
     # Ensure user-defined spatial references for outputs are correctly parsed.
     # Certain options require normalization to a space not explicitly defined by users.
     # These spaces will not be included in the final outputs.
diff --git a/fmriprep/tests/test_config.py b/fmriprep/tests/test_config.py
index c43513657..13812bb81 100644
--- a/fmriprep/tests/test_config.py
+++ b/fmriprep/tests/test_config.py
@@ -39,3 +39,15 @@ def test_config_spaces():
         format_reference((s.fullname, s.spec))
         for s in spaces.references if s.standard and s.dim == 3
     ]
+
+    config.execution.output_spaces = None
+    config.workflow.use_aroma = False
+    config.init_spaces()
+    spaces = config.workflow.spaces
+
+    assert [str(s) for s in spaces.get_standard(full_spec=True)] == []
+
+    assert [
+        format_reference((s.fullname, s.spec))
+        for s in spaces.references if s.standard and s.dim == 3
+    ] == ['MNI152NLin2009cAsym']

From baeb1d6aaac79452ccba9d48ced7f585322a86f2 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 23:02:21 -0700
Subject: [PATCH 39/43] fix: apply @mgxd's suggestions

---
 fmriprep/cli/workflow.py | 13 ++++---------
 1 file changed, 4 insertions(+), 9 deletions(-)

diff --git a/fmriprep/cli/workflow.py b/fmriprep/cli/workflow.py
index 6a3ddc55c..053791de1 100644
--- a/fmriprep/cli/workflow.py
+++ b/fmriprep/cli/workflow.py
@@ -106,12 +106,12 @@ def build_boilerplate(config_file, workflow):
     config.load(config_file)
     logs_path = config.execution.output_dir / 'fmriprep' / 'logs'
     boilerplate = workflow.visit_desc()
+    citation_files = {
+        ext: logs_path / ('CITATION.%s' % ext)
+        for ext in ('bib', 'tex', 'md', 'html')
+    }
 
     if boilerplate:
-        citation_files = {
-            ext: logs_path / ('CITATION.%s' % ext)
-            for ext in ('bib', 'tex', 'md', 'html')
-        }
         # To please git-annex users and also to guarantee consistency
         # among different renderings of the same file, first remove any
         # existing one
@@ -123,11 +123,6 @@ def build_boilerplate(config_file, workflow):
 
     citation_files['md'].write_text(boilerplate)
 
-    citation_files = {
-        ext: config.execution.output_dir / 'fmriprep' / 'logs'
-        / ('CITATION.%s' % ext) for ext in ('bib', 'tex', 'md', 'html')
-    }
-
     if not config.execution.md_only_boilerplate and citation_files['md'].exists():
         from subprocess import check_call, CalledProcessError, TimeoutExpired
         from pkg_resources import resource_filename as pkgrf

From 969dca7a0b788eca444cd96b59af2c28a0a96cd2 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Tue, 10 Mar 2020 11:14:28 -0700
Subject: [PATCH 40/43] Update fmriprep/workflows/bold/base.py [skip ci]

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 fmriprep/workflows/bold/base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/workflows/bold/base.py b/fmriprep/workflows/bold/base.py
index 71d382e80..d02495093 100644
--- a/fmriprep/workflows/bold/base.py
+++ b/fmriprep/workflows/bold/base.py
@@ -309,7 +309,7 @@ def init_func_preproc_wf(bold_file):
     ])
 
     # Generate a tentative boldref
-    bold_reference_wf = init_bold_reference_wf(omp_nthreads=config.nipype.omp_nthreads)
+    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
     bold_reference_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
     if sbref_file is not None:
         workflow.connect([

From a795760dc4005219fcbd8fc2ca50644538035738 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Mon, 9 Mar 2020 23:05:55 -0700
Subject: [PATCH 41/43] sty: pacify flake8 [skip ci]

---
 fmriprep/cli/parser.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index c66af6b03..f4c934179 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -16,7 +16,7 @@ def _build_parser():
     )
     from packaging.version import Version
     from .version import check_latest, is_flagged
-    from niworkflows.utils.spaces import Reference, SpatialReferences, OutputReferencesAction
+    from niworkflows.utils.spaces import Reference, OutputReferencesAction
 
     def _path_exists(path, parser):
         """Ensure a given path exists."""

From 981d36c08f92ad98200b5271e1bb44d1bdab1fcc Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 10 Mar 2020 11:09:14 -0700
Subject: [PATCH 42/43] maint: add comments regarding building workflow and
 save/load config [skip ci]

addresses https://github.com/poldracklab/fmriprep/pull/2018#discussion_r390406077

also address https://github.com/poldracklab/fmriprep/pull/2018#discussion_r390418416
---
 fmriprep/cli/run.py | 10 +++++++++-
 fmriprep/config.py  |  2 +-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index cfd33671a..3a9f8e57c 100755
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -21,10 +21,15 @@ def main():
         from ..utils.sentry import sentry_setup
         sentry_setup()
 
+    # CRITICAL Save the config to a file. This is necessary because the execution graph
+    # is built as a separate process to keep the memory footprint low. The most
+    # straightforward way to communicate with the child process is via the filesystem.
     config_file = config.execution.work_dir / '.fmriprep.toml'
     config.to_filename(config_file)
 
-    # Call build_workflow(config_file, retval) in a subprocess
+    # CRITICAL Call build_workflow(config_file, retval) in a subprocess.
+    # Because Python on Linux does not ever free virtual memory (VM), running the
+    # workflow construction jailed within a process preempts excessive VM buildup.
     with Manager() as mgr:
         from .workflow import build_workflow
         retval = mgr.dict()
@@ -35,6 +40,9 @@ def main():
         retcode = p.exitcode or retval.get('return_code', 0)
         fmriprep_wf = retval.get('workflow', None)
 
+    # CRITICAL Load the config from the file. This is necessary because the ``build_workflow``
+    # function executed constrained in a process may change the config (and thus the global
+    # state of fMRIPrep).
     config.load(config_file)
 
     if config.execution.reports_only:
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 67428b0ee..998f4a6f6 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -86,7 +86,7 @@
     pass  # context has been already set
 finally:
     # Defer all custom import for after initializing the forkserver and
-    # redirecting warnings
+    # ignoring the most annoying warnings
     import os
     import sys
     import logging

From 4d55e587d515af72bbc73a51f8d200972763409d Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Tue, 10 Mar 2020 11:17:21 -0700
Subject: [PATCH 43/43] fix(circle): remove setting nipype log format - should
 be handled by config

At some point of this PR (#2018), I was getting pklz crashfiles.
Obviously, the config wasn't working properly. Once that was addressed via
https://github.com/poldracklab/fmriprep/pull/2018/commits/8a0bf9d77dee8d557c92dd149e8eb7cc6a053a61,
this setting should go away for us to identify any regression of the
problem.
---
 .circleci/config.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index b1fcbc1ba..faec4dc1b 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -166,7 +166,6 @@ jobs:
             printf "[execution]\nstop_on_first_crash = true\n" > /tmp/ds005/nipype.cfg
             echo "poll_sleep_duration = 0.01" >> /tmp/ds005/nipype.cfg
             echo "hash_method = content" >> /tmp/ds005/nipype.cfg
-            echo "crashfile_format = txt" >> /tmp/ds005/nipype.cfg
             cp /tmp/ds005/nipype.cfg /tmp/ds054/nipype.cfg
             cp /tmp/ds005/nipype.cfg /tmp/ds210/nipype.cfg
       - persist_to_workspace: