resampling.py

# -*- 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:
"""
Resampling workflows
++++++++++++++++++++

.. autofunction:: init_bold_surf_wf
.. autofunction:: init_bold_std_trans_wf
.. autofunction:: init_bold_preproc_trans_wf

"""
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu, freesurfer as fs
from nipype.interfaces.fsl import Split as FSLSplit

from niworkflows.engine.workflows import LiterateWorkflow as Workflow
from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms
from niworkflows.interfaces.freesurfer import (
    MedialNaNs,
    # See https://github.com/poldracklab/fmriprep/issues/768
    PatchedConcatenateLTA as ConcatenateLTA,
    PatchedLTAConvert as LTAConvert
)
from niworkflows.interfaces.itk import MultiApplyTransforms
from niworkflows.interfaces.utils import GenerateSamplingReference
from niworkflows.interfaces.utility import KeySelect
from niworkflows.interfaces.surf import GiftiSetAnatomicalStructure

from ...interfaces import DerivativesDataSink
from ...interfaces.nilearn import Merge

from .util import init_bold_reference_wf

DEFAULT_MEMORY_MIN_GB = 0.01
NONSTANDARD_REFERENCES = ['anat', 'T1w', 'run', 'func', 'sbref', 'fsnative']


def init_bold_surf_wf(mem_gb, output_spaces, medial_surface_nan, name='bold_surf_wf'):
    """
    This workflow samples functional images to FreeSurfer surfaces

    For each vertex, the cortical ribbon is sampled at six points (spaced 20% of thickness apart)
    and averaged.

    Outputs are in GIFTI format.

    .. workflow::
        :graph2use: colored
        :simple_form: yes

        from fmriprep.workflows.bold import init_bold_surf_wf
        wf = init_bold_surf_wf(mem_gb=0.1,
                               output_spaces=['T1w', 'fsnative',
                                             'template', 'fsaverage5'],
                               medial_surface_nan=False)

    **Parameters**

        output_spaces : list
            List of output spaces functional images are to be resampled to
            Target spaces beginning with ``fs`` will be selected for resampling,
            such as ``fsaverage`` or related template spaces
            If the list contains ``fsnative``, images will be resampled to the
            individual subject's native surface
        medial_surface_nan : bool
            Replace medial wall values with NaNs on functional GIFTI files

    **Inputs**

        source_file
            Motion-corrected BOLD series in T1 space
        t1_preproc
            Bias-corrected structural template image
        subjects_dir
            FreeSurfer SUBJECTS_DIR
        subject_id
            FreeSurfer subject ID
        t1_2_fsnative_forward_transform
            LTA-style affine matrix translating from T1w to FreeSurfer-conformed subject space

    **Outputs**

        surfaces
            BOLD series, resampled to FreeSurfer surfaces

    """
    # Ensure volumetric spaces do not sneak into this workflow
    spaces = [space for space in output_spaces if space.startswith('fs')]

    workflow = Workflow(name=name)

    if spaces:
        workflow.__desc__ = """\
The BOLD time-series, were resampled to surfaces on the following
spaces: {out_spaces}.
""".format(out_spaces=', '.join(['*%s*' % s for s in spaces]))
    inputnode = pe.Node(
        niu.IdentityInterface(fields=['source_file', 't1_preproc', 'subject_id', 'subjects_dir',
                                      't1_2_fsnative_forward_transform']),
        name='inputnode')

    outputnode = pe.Node(niu.IdentityInterface(fields=['surfaces']), name='outputnode')

    def select_target(subject_id, space):
        """ Given a source subject ID and a target space, get the target subject ID """
        return subject_id if space == 'fsnative' else space

    targets = pe.MapNode(niu.Function(function=select_target),
                         iterfield=['space'], name='targets',
                         mem_gb=DEFAULT_MEMORY_MIN_GB)
    targets.inputs.space = spaces

    # Rename the source file to the output space to simplify naming later
    rename_src = pe.MapNode(niu.Rename(format_string='%(subject)s', keep_ext=True),
                            iterfield='subject', name='rename_src', run_without_submitting=True,
                            mem_gb=DEFAULT_MEMORY_MIN_GB)
    rename_src.inputs.subject = spaces

    resampling_xfm = pe.Node(LTAConvert(in_lta='identity.nofile', out_lta=True),
                             name='resampling_xfm')
    set_xfm_source = pe.Node(ConcatenateLTA(out_type='RAS2RAS'), name='set_xfm_source')

    sampler = pe.MapNode(
        fs.SampleToSurface(sampling_method='average', sampling_range=(0, 1, 0.2),
                           sampling_units='frac', interp_method='trilinear', cortex_mask=True,
                           override_reg_subj=True, out_type='gii'),
        iterfield=['source_file', 'target_subject'],
        iterables=('hemi', ['lh', 'rh']),
        name='sampler', mem_gb=mem_gb * 3)

    medial_nans = pe.MapNode(MedialNaNs(), iterfield=['in_file', 'target_subject'],
                             name='medial_nans', mem_gb=DEFAULT_MEMORY_MIN_GB)

    merger = pe.JoinNode(niu.Merge(1, ravel_inputs=True), name='merger',
                         joinsource='sampler', joinfield=['in1'], run_without_submitting=True,
                         mem_gb=DEFAULT_MEMORY_MIN_GB)

    update_metadata = pe.MapNode(GiftiSetAnatomicalStructure(), iterfield='in_file',
                                 name='update_metadata', mem_gb=DEFAULT_MEMORY_MIN_GB)

    workflow.connect([
        (inputnode, targets, [('subject_id', 'subject_id')]),
        (inputnode, rename_src, [('source_file', 'in_file')]),
        (inputnode, resampling_xfm, [('source_file', 'source_file'),
                                     ('t1_preproc', 'target_file')]),
        (inputnode, set_xfm_source, [('t1_2_fsnative_forward_transform', 'in_lta2')]),
        (resampling_xfm, set_xfm_source, [('out_lta', 'in_lta1')]),
        (inputnode, sampler, [('subjects_dir', 'subjects_dir'),
                              ('subject_id', 'subject_id')]),
        (set_xfm_source, sampler, [('out_file', 'reg_file')]),
        (targets, sampler, [('out', 'target_subject')]),
        (rename_src, sampler, [('out_file', 'source_file')]),
        (merger, update_metadata, [('out', 'in_file')]),
        (update_metadata, outputnode, [('out_file', 'surfaces')]),
    ])

    if medial_surface_nan:
        workflow.connect([
            (inputnode, medial_nans, [('subjects_dir', 'subjects_dir')]),
            (sampler, medial_nans, [('out_file', 'in_file')]),
            (targets, medial_nans, [('out', 'target_subject')]),
            (medial_nans, merger, [('out_file', 'in1')]),
        ])
    else:
        workflow.connect(sampler, 'out_file', merger, 'in1')

    return workflow


def init_bold_std_trans_wf(
    freesurfer,
    mem_gb,
    omp_nthreads,
    standard_spaces,
    name='bold_std_trans_wf',
    use_compression=True,
    use_fieldwarp=False
):
    """
    This workflow samples functional images into standard space with a single
    resampling of the original BOLD series.

    .. workflow::
        :graph2use: colored
        :simple_form: yes

        from collections import OrderedDict
        from fmriprep.workflows.bold import init_bold_std_trans_wf
        wf = init_bold_std_trans_wf(
            freesurfer=True,
            mem_gb=3,
            omp_nthreads=1,
            standard_spaces=OrderedDict([('MNI152Lin', {}),
                                         ('fsaverage', {'density': '10k'})]),
        )

    **Parameters**

        freesurfer : bool
            Whether to generate FreeSurfer's aseg/aparc segmentations on BOLD space.
        mem_gb : float
            Size of BOLD file in GB
        omp_nthreads : int
            Maximum number of threads an individual process may use
        standard_spaces : OrderedDict
            Ordered dictionary where keys are TemplateFlow ID strings (e.g.,
            ``MNI152Lin``, ``MNI152NLin6Asym``, ``MNI152NLin2009cAsym``, or ``fsLR``),
            or paths pointing to custom templates organized in a TemplateFlow-like structure.
            Values of the dictionary aggregate modifiers (e.g., the value for the key ``MNI152Lin``
            could be ``{'resolution': 2}`` if one wants the resampling to be done on the 2mm
            resolution version of the selected template).
        name : str
            Name of workflow (default: ``bold_std_trans_wf``)
        use_compression : bool
            Save registered BOLD series as ``.nii.gz``
        use_fieldwarp : bool
            Include SDC warp in single-shot transform from BOLD to MNI

    **Inputs**

        anat2std_xfm
            List of anatomical-to-standard space transforms generated during
            spatial normalization.
        bold_aparc
            FreeSurfer's ``aparc+aseg.mgz`` atlas projected into the T1w reference
            (only if ``recon-all`` was run).
        bold_aseg
            FreeSurfer's ``aseg.mgz`` atlas projected into the T1w reference
            (only if ``recon-all`` was run).
        bold_mask
            Skull-stripping mask of reference image
        bold_split
            Individual 3D volumes, not motion corrected
        fieldwarp
            a :abbr:`DFM (displacements field map)` in ITK format
        hmc_xforms
            List of affine transforms aligning each volume to ``ref_image`` in ITK format
        itk_bold_to_t1
            Affine transform from ``ref_bold_brain`` to T1 space (ITK format)
        name_source
            BOLD series NIfTI file
            Used to recover original information lost during processing
        templates
            List of templates that were applied as targets during
            spatial normalization.

    **Outputs** - Two outputnodes are available. One output node (with name ``poutputnode``)
    will be parameterized in a Nipype sense (see `Nipype iterables
    <https://miykael.github.io/nipype_tutorial/notebooks/basic_iteration.html>`__), and a
    second node (``outputnode``) will collapse the parameterized outputs into synchronous
    lists of the following fields:

        bold_std
            BOLD series, resampled to template space
        bold_std_ref
            Reference, contrast-enhanced summary of the BOLD series, resampled to template space
        bold_mask_std
            BOLD series mask in template space
        bold_aseg_std
            FreeSurfer's ``aseg.mgz`` atlas, in template space at the BOLD resolution
            (only if ``recon-all`` was run)
        bold_aparc_std
            FreeSurfer's ``aparc+aseg.mgz`` atlas, in template space at the BOLD resolution
            (only if ``recon-all`` was run)
        templates
            Template identifiers synchronized correspondingly to previously
            described outputs.

    """

    # Filter ``standard_spaces``
    vol_std_spaces = [k for k in standard_spaces.keys() if not k.startswith('fs')]

    workflow = Workflow(name=name)

    if len(vol_std_spaces) == 1:
        workflow.__desc__ = """\
The BOLD time-series were resampled into standard space,
generating a *preprocessed BOLD run in {tpl} space*.
""".format(tpl=vol_std_spaces)
    else:
        workflow.__desc__ = """\
The BOLD time-series were resampled into several standard spaces,
correspondingly generating the following *spatially-normalized,
preprocessed BOLD runs*: {tpl}.
""".format(tpl=', '.join(vol_std_spaces))

    inputnode = pe.Node(
        niu.IdentityInterface(fields=[
            'anat2std_xfm',
            'bold_aparc',
            'bold_aseg',
            'bold_mask',
            'bold_split',
            'fieldwarp',
            'hmc_xforms',
            'itk_bold_to_t1',
            'name_source',
            'templates',
        ]),
        name='inputnode'
    )

    select_std = pe.Node(KeySelect(
        fields=['resolution', 'anat2std_xfm']),
        name='select_std', run_without_submitting=True)

    select_std.inputs.resolution = [v.get('resolution') or v.get('res') or 'native'
                                    for k, v in list(standard_spaces.items())
                                    if k in vol_std_spaces]
    select_std.iterables = ('key', vol_std_spaces)

    select_tpl = pe.Node(niu.Function(function=_select_template),
                         name='select_tpl', run_without_submitting=True)
    select_tpl.inputs.template_specs = standard_spaces

    gen_ref = pe.Node(GenerateSamplingReference(), name='gen_ref',
                      mem_gb=0.3)  # 256x256x256 * 64 / 8 ~ 150MB)

    mask_std_tfm = pe.Node(
        ApplyTransforms(interpolation='MultiLabel', float=True),
        name='mask_std_tfm',
        mem_gb=1
    )

    # Write corrected file in the designated output dir
    mask_merge_tfms = pe.Node(niu.Merge(2), name='mask_merge_tfms', run_without_submitting=True,
                              mem_gb=DEFAULT_MEMORY_MIN_GB)

    workflow.connect([
        (inputnode, select_std, [('templates', 'keys'),
                                 ('anat2std_xfm', 'anat2std_xfm')]),
        (inputnode, mask_std_tfm, [('bold_mask', 'input_image')]),
        (inputnode, gen_ref, [(('bold_split', _first), 'moving_image')]),
        (inputnode, mask_merge_tfms, [(('itk_bold_to_t1', _aslist), 'in2')]),
        (select_std, select_tpl, [('key', 'template')]),
        (select_std, mask_merge_tfms, [('anat2std_xfm', 'in1')]),
        (select_std, gen_ref, [(('resolution', _is_native), 'keep_native')]),
        (select_tpl, gen_ref, [('out', 'fixed_image')]),
        (mask_merge_tfms, mask_std_tfm, [('out', 'transforms')]),
        (gen_ref, mask_std_tfm, [('out_file', 'reference_image')]),
    ])

    nxforms = 4 if use_fieldwarp else 3
    merge_xforms = pe.Node(niu.Merge(nxforms), name='merge_xforms',
                           run_without_submitting=True, mem_gb=DEFAULT_MEMORY_MIN_GB)
    workflow.connect([(inputnode, merge_xforms, [('hmc_xforms', 'in%d' % nxforms)])])

    if use_fieldwarp:
        workflow.connect([(inputnode, merge_xforms, [('fieldwarp', 'in3')])])

    bold_to_std_transform = pe.Node(
        MultiApplyTransforms(interpolation="LanczosWindowedSinc", float=True, copy_dtype=True),
        name='bold_to_std_transform', mem_gb=mem_gb * 3 * omp_nthreads, n_procs=omp_nthreads)

    merge = pe.Node(Merge(compress=use_compression), name='merge',
                    mem_gb=mem_gb * 3)

    # Generate a reference on the target T1w space
    gen_final_ref = init_bold_reference_wf(
        omp_nthreads=omp_nthreads, pre_mask=True)

    workflow.connect([
        (inputnode, merge_xforms, [
            (('itk_bold_to_t1', _aslist), 'in2')]),
        (inputnode, merge, [('name_source', 'header_source')]),
        (inputnode, bold_to_std_transform, [('bold_split', 'input_image')]),
        (select_std, merge_xforms, [('anat2std_xfm', 'in1')]),
        (merge_xforms, bold_to_std_transform, [('out', 'transforms')]),
        (gen_ref, bold_to_std_transform, [('out_file', 'reference_image')]),
        (bold_to_std_transform, merge, [('out_files', 'in_files')]),
        (merge, gen_final_ref, [('out_file', 'inputnode.bold_file')]),
        (mask_std_tfm, gen_final_ref, [('output_image', 'inputnode.bold_mask')]),
    ])

    # Connect output nodes
    output_names = ['bold_std', 'bold_std_ref', 'bold_mask_std', 'templates']
    if freesurfer:
        output_names += ['bold_aseg_std', 'bold_aparc_std']

    # poutputnode - parametric output node
    poutputnode = pe.Node(niu.IdentityInterface(fields=output_names),
                          name='poutputnode')

    workflow.connect([
        (gen_final_ref, poutputnode, [('outputnode.ref_image', 'bold_std_ref')]),
        (merge, poutputnode, [('out_file', 'bold_std')]),
        (mask_std_tfm, poutputnode, [('output_image', 'bold_mask_std')]),
        (select_std, poutputnode, [('key', 'templates')]),
    ])

    if freesurfer:
        # Sample the parcellation files to functional space
        aseg_std_tfm = pe.Node(
            ApplyTransforms(interpolation='MultiLabel', float=True),
            name='aseg_std_tfm', mem_gb=1)
        aparc_std_tfm = pe.Node(
            ApplyTransforms(interpolation='MultiLabel', float=True),
            name='aparc_std_tfm', mem_gb=1)

        workflow.connect([
            (inputnode, aseg_std_tfm, [('bold_aseg', 'input_image')]),
            (inputnode, aparc_std_tfm, [('bold_aparc', 'input_image')]),
            (select_std, aseg_std_tfm, [('anat2std_xfm', 'transforms')]),
            (select_std, aparc_std_tfm, [('anat2std_xfm', 'transforms')]),
            (gen_ref, aseg_std_tfm, [('out_file', 'reference_image')]),
            (gen_ref, aparc_std_tfm, [('out_file', 'reference_image')]),
            (aseg_std_tfm, poutputnode, [('output_image', 'bold_aseg_std')]),
            (aparc_std_tfm, poutputnode, [('output_image', 'bold_aparc_std')]),
        ])

    # Connect outputnode to the parameterized outputnode
    outputnode = pe.JoinNode(niu.IdentityInterface(fields=output_names),
                             name='outputnode', joinsource='select_std')
    workflow.connect([
        (poutputnode, outputnode, [(f, f) for f in output_names])
    ])

    return workflow


def init_bold_preproc_trans_wf(mem_gb, omp_nthreads,
                               name='bold_preproc_trans_wf',
                               use_compression=True,
                               use_fieldwarp=False,
                               split_file=False,
                               interpolation='LanczosWindowedSinc'):
    """
    This workflow resamples the input fMRI in its native (original)
    space in a "single shot" from the original BOLD series.

    .. workflow::
        :graph2use: colored
        :simple_form: yes

        from fmriprep.workflows.bold import init_bold_preproc_trans_wf
        wf = init_bold_preproc_trans_wf(mem_gb=3, omp_nthreads=1)

    **Parameters**

        mem_gb : float
            Size of BOLD file in GB
        omp_nthreads : int
            Maximum number of threads an individual process may use
        name : str
            Name of workflow (default: ``bold_std_trans_wf``)
        use_compression : bool
            Save registered BOLD series as ``.nii.gz``
        use_fieldwarp : bool
            Include SDC warp in single-shot transform from BOLD to MNI
        split_file : bool
            Whether the input file should be splitted (it is a 4D file)
            or it is a list of 3D files (default ``False``, do not split)
        interpolation : str
            Interpolation type to be used by ANTs' ``applyTransforms``
            (default ``'LanczosWindowedSinc'``)

    **Inputs**

        bold_file
            Individual 3D volumes, not motion corrected
        bold_mask
            Skull-stripping mask of reference image
        name_source
            BOLD series NIfTI file
            Used to recover original information lost during processing
        hmc_xforms
            List of affine transforms aligning each volume to ``ref_image`` in ITK format
        fieldwarp
            a :abbr:`DFM (displacements field map)` in ITK format

    **Outputs**

        bold
            BOLD series, resampled in native space, including all preprocessing
        bold_mask
            BOLD series mask calculated with the new time-series
        bold_ref
            BOLD reference image: an average-like 3D image of the time-series
        bold_ref_brain
            Same as ``bold_ref``, but once the brain mask has been applied

    """
    workflow = Workflow(name=name)
    workflow.__desc__ = """\
The BOLD time-series (including slice-timing correction when applied)
were resampled onto their original, native space by applying
{transforms}.
These resampled BOLD time-series will be referred to as *preprocessed
BOLD in original space*, or just *preprocessed BOLD*.
""".format(transforms="""\
a single, composite transform to correct for head-motion and
susceptibility distortions""" if use_fieldwarp else """\
the transforms to correct for head-motion""")

    inputnode = pe.Node(niu.IdentityInterface(fields=[
        'name_source', 'bold_file', 'bold_mask', 'hmc_xforms', 'fieldwarp']),
        name='inputnode'
    )

    outputnode = pe.Node(
        niu.IdentityInterface(fields=['bold', 'bold_mask', 'bold_ref', 'bold_ref_brain']),
        name='outputnode')

    bold_transform = pe.Node(
        MultiApplyTransforms(interpolation=interpolation, float=True, copy_dtype=True),
        name='bold_transform', mem_gb=mem_gb * 3 * omp_nthreads, n_procs=omp_nthreads)

    merge = pe.Node(Merge(compress=use_compression), name='merge',
                    mem_gb=mem_gb * 3)

    # Generate a new BOLD reference
    bold_reference_wf = init_bold_reference_wf(omp_nthreads=omp_nthreads)
    bold_reference_wf.__desc__ = None  # Unset description to avoid second appearance

    workflow.connect([
        (inputnode, merge, [('name_source', 'header_source')]),
        (bold_transform, merge, [('out_files', 'in_files')]),
        (merge, bold_reference_wf, [('out_file', 'inputnode.bold_file')]),
        (merge, outputnode, [('out_file', 'bold')]),
        (bold_reference_wf, outputnode, [
            ('outputnode.ref_image', 'bold_ref'),
            ('outputnode.ref_image_brain', 'bold_ref_brain'),
            ('outputnode.bold_mask', 'bold_mask')]),
    ])

    # Input file is not splitted
    if split_file:
        bold_split = pe.Node(FSLSplit(dimension='t'), name='bold_split',
                             mem_gb=mem_gb * 3)
        workflow.connect([
            (inputnode, bold_split, [('bold_file', 'in_file')]),
            (bold_split, bold_transform, [
                ('out_files', 'input_image'),
                (('out_files', _first), 'reference_image'),
            ])
        ])
    else:
        workflow.connect([
            (inputnode, bold_transform, [('bold_file', 'input_image'),
                                         (('bold_file', _first), 'reference_image')]),
        ])

    if use_fieldwarp:
        merge_xforms = pe.Node(niu.Merge(2), name='merge_xforms',
                               run_without_submitting=True, mem_gb=DEFAULT_MEMORY_MIN_GB)
        workflow.connect([
            (inputnode, merge_xforms, [('fieldwarp', 'in1'),
                                       ('hmc_xforms', 'in2')]),
            (merge_xforms, bold_transform, [('out', 'transforms')]),
        ])
    else:
        def _aslist(val):
            return [val]
        workflow.connect([
            (inputnode, bold_transform, [(('hmc_xforms', _aslist), 'transforms')]),
        ])

    # Code ready to generate a pre/post processing report
    # bold_bold_report_wf = init_bold_preproc_report_wf(
    #     mem_gb=mem_gb['resampled'],
    #     reportlets_dir=reportlets_dir
    # )
    # workflow.connect([
    #     (inputnode, bold_bold_report_wf, [
    #         ('bold_file', 'inputnode.name_source'),
    #         ('bold_file', 'inputnode.in_pre')]),  # This should be after STC
    #     (bold_bold_trans_wf, bold_bold_report_wf, [
    #         ('outputnode.bold', 'inputnode.in_post')]),
    # ])

    return workflow


def init_bold_preproc_report_wf(mem_gb, reportlets_dir, name='bold_preproc_report_wf'):
    """
    This workflow generates and saves a reportlet showing the effect of resampling
    the BOLD signal using the standard deviation maps.

    .. workflow::
        :graph2use: orig
        :simple_form: yes

        from fmriprep.workflows.bold.resampling import init_bold_preproc_report_wf
        wf = init_bold_preproc_report_wf(mem_gb=1, reportlets_dir='.')

    **Parameters**

        mem_gb : float
            Size of BOLD file in GB
        reportlets_dir : str
            Directory in which to save reportlets
        name : str, optional
            Workflow name (default: bold_preproc_report_wf)

    **Inputs**

        in_pre
            BOLD time-series, before resampling
        in_post
            BOLD time-series, after resampling
        name_source
            BOLD series NIfTI file
            Used to recover original information lost during processing

    """

    from nipype.algorithms.confounds import TSNR
    from niworkflows.interfaces import SimpleBeforeAfter

    workflow = Workflow(name=name)

    inputnode = pe.Node(niu.IdentityInterface(
        fields=['in_pre', 'in_post', 'name_source']), name='inputnode')

    pre_tsnr = pe.Node(TSNR(), name='pre_tsnr', mem_gb=mem_gb * 4.5)
    pos_tsnr = pe.Node(TSNR(), name='pos_tsnr', mem_gb=mem_gb * 4.5)

    bold_rpt = pe.Node(SimpleBeforeAfter(), name='bold_rpt',
                       mem_gb=0.1)
    ds_report_bold = pe.Node(
        DerivativesDataSink(base_directory=reportlets_dir, desc='preproc',
                            keep_dtype=True), name='ds_report_bold',
        mem_gb=DEFAULT_MEMORY_MIN_GB,
        run_without_submitting=True
    )

    workflow.connect([
        (inputnode, ds_report_bold, [('name_source', 'source_file')]),
        (inputnode, pre_tsnr, [('in_pre', 'in_file')]),
        (inputnode, pos_tsnr, [('in_post', 'in_file')]),
        (pre_tsnr, bold_rpt, [('stddev_file', 'before')]),
        (pos_tsnr, bold_rpt, [('stddev_file', 'after')]),
        (bold_rpt, ds_report_bold, [('out_report', 'in_file')]),
    ])

    return workflow


def _select_template(template, template_specs):
    from niworkflows.utils.misc import get_template_specs
    specs = template_specs[template]
    specs['suffix'] = specs.get('suffix', 'T1w')
    return get_template_specs(template, template_spec=specs)[0]


def _first(inlist):
    return inlist[0]


def _aslist(in_value):
    if isinstance(in_value, list):
        return in_value
    return [in_value]


def _is_native(in_value):
    return in_value == 'native'


def _tpl_res(in_value):
    if in_value == 'native':
        return 2
    return in_value