<reponame>Neurita/pypes
# -*- coding: utf-8 -*-
"""
Functions to create pipelines for public and not so public available datasets.
"""

from collections import OrderedDict

from neuro_pypes.io import build_crumb_workflow
from neuro_pypes.config import update_config
from neuro_pypes.anat import (
    attach_spm_anat_preprocessing,
    attach_ants_cortical_thickness
)
from neuro_pypes.dmri import (
    attach_spm_fsl_dti_preprocessing,
    attach_camino_tractography
)
from neuro_pypes.fmri import (
    attach_rest_preprocessing,
    attach_rest_grptemplate_preprocessing
)
from neuro_pypes.pet import (
    attach_spm_mrpet_preprocessing,
    attach_spm_pet_preprocessing,
    attach_spm_pet_grouptemplate
)


def _cobre_wf_setup(wf_name):
    """ Return a list of workflow-attach functions and a dict with kwargs for
    the `in_out_crumb_wf` function to run workflows against the COBRE database.

    Parameters
    ----------
    wf_name

    Returns
    -------
    wf_attachers: dict with wf attacher functions

    wf_params: dict with configuration parameters for the workflows.
        Use this only to fixed configurations needed for the correct functioning of the workflows.

    files_crumb_args: dict with kwargs
        This arguments are for the in_out_crumb_wf.
        A dict that declares the values each file type the crumb arguments in `data_crumb` must be replaced with.
        Example:
              {'anat':  [('modality', 'anat_1'),
                         ('image',    'mprage.nii.gz')],
              'rest':   [('modality', 'rest_1'),
                         ('image',    'rest.nii.gz')],
              }
    """
    attach_functions = {
        "spm_anat_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing)
        ],

        "spm_anat_rest_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_rest_preproc", attach_rest_preprocessing),
        ],
    }

    if wf_name not in attach_functions:
        raise KeyError('Expected an existing pipeline name, got {}. '
                       'Available options: {}'.format(wf_name, list(attach_functions.keys())))

    files_crumb_args = {
        'anat': [('modality', 'anat_1'),
                 ('image', 'mprage.nii.gz')]
    }  # 'anat_1/mprage.nii.gz',

    if 'rest' in wf_name:
        files_crumb_args.update({
            'rest': [('modality', 'rest_1'),
                     ('image', 'rest.nii.gz')
                     ],  # 'rest_1/rest.nii.gz'},
        })

    params = {'file_templates': files_crumb_args}

    return OrderedDict(attach_functions[wf_name]), params


def _clinical_wf_setup(wf_name):
    """ Return a list of workflow-attach functions and a dict with kwargs for
    the `in_out_crumb_wf` function to run workflows against the clinical database.

    Parameters
    ----------
    wf_name

    Returns
    -------
    wf_attachers: dict with wf attacher functions

    wf_params: dict with configuration parameters for the workflows.
        Use this only to fixed configurations needed for the correct functioning of the workflows.

    files_crumb_args: dict with kwargs
        This arguments are for the in_out_crumb_wf.
        A dict that declares the values each file type the crumb arguments in `data_crumb` must be replaced with.
        Example:
              {'anat':  [('modality', 'anat_1'),
                         ('image',    'mprage.nii.gz')],
              'rest':   [('modality', 'rest_1'),
                         ('image',    'rest.nii.gz')],
              }
    """
    # MPRAGE bias-field correction, normalization to MNI, and tissue segmentation
    attach_functions = {
        "spm_anat_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing)
        ],

        # PET normalization to MNI
        "spm_pet_preproc": [
            ("spm_pet_preproc", attach_spm_pet_preprocessing)
        ],

        # will create a PET group template
        "spm_pet_template": [
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
        ],

        # MPRAGE preprocessing, PET MNI group template, PET PVC, and PET normalization to group template
        "spm_anat_pet_tpm_pvc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
        ],

        # MPRAGE preprocessing, PET MNI group template, PET PVC, and rest-fMRI
        "spm_anat_pet_pvc_rest": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
            ("spm_rest_preproc", attach_rest_preprocessing),
        ],

        # MPRAGE preprocessing, PET PVC, and PET normalization to MNI
        "spm_anat_pet_pvc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_mrpet_preproc", attach_spm_mrpet_preprocessing),
        ],

        # MPRAGE preprocessing, rs-fMRI preprocessing and normalization to MNI
        "spm_anat_rest_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_rest_preproc", attach_rest_preprocessing),
        ],

        # MPRAGE preprocessing, DTI preprocessing with FSL
        "fsl_dti_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("fsl_dti_preproc", attach_spm_fsl_dti_preprocessing),
        ],

        # MPRAGE preprocessing, DTI preprocessing with FSL, and tractography with Camino
        "anat_dti_camino": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("fsl_dti_preproc", attach_spm_fsl_dti_preprocessing),
            ("camino_tract", attach_camino_tractography),
        ],

        # MPRAGE and PET preprocessing, DTI preprocessing with FSL, and tractography with Camino
        "anat_pet_dti_camino": [("spm_anat_preproc", attach_spm_anat_preprocessing),
                                ("spm_mrpet_preproc", attach_spm_mrpet_preprocessing),
                                ("fsl_dti_preproc", attach_spm_fsl_dti_preprocessing),
                                ("camino_tract", attach_camino_tractography),
                                ],

        # MPRAGE preprocessing, and EPI group template
        "spm_anat_rest_tpm_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_warp_fmri", attach_rest_grptemplate_preprocessing),
        ],

        # MPRAGE preprocessing, EPI and PET group template, and PET and rs-fMRI preprocessing and
        # normalization to group template
        "spm_anat_pet_rest_tpm_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_warp_fmri", attach_rest_grptemplate_preprocessing),
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
        ],

        # MPRAGE preprocessing, EPI group template, and rs-fMRI preprocessing and normalization to MNI
        "spm_anat_pet_rest_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_rest_preproc", attach_rest_preprocessing),
            ("spm_pet_preproc", attach_spm_mrpet_preprocessing),
        ],

        # MPRAGE and cortical thickness
        "spm_anat_ants_cortical_thick": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("ants_cort_thick", attach_ants_cortical_thickness),
        ],
    }

    parameters = {
        "spm_pet_template": [('spm_pet_template.do_petpvc', False), ],
        "spm_anat_pet_tpm_pvc": [('spm_pet_template.do_petpvc', True), ],
    }

    if wf_name not in attach_functions:
        raise KeyError('Expected an existing pipeline name, got {}. '
                       'Available options: {}'.format(wf_name, list(attach_functions.keys())))

    # the pipeline parameters
    wf_params = parameters.get(wf_name, None)
    if wf_params is not None:
        wf_params = dict(wf_params)

    # the input files crumb patterns
    files_crumb_args = {}
    files_crumb_args.update({'anat': [('image', 'anat_hc.nii.gz')]})

    if 'pet' in wf_name:
        files_crumb_args.update({'pet': [('image', 'pet_fdg.nii.gz')], })

    if 'rest' in wf_name:
        files_crumb_args.update({'rest': [('image', 'rest.nii.gz')], })

    if 'dti' in wf_name:
        files_crumb_args.update({
            'diff': [('image', 'diff.nii.gz')],
            'bval': [('image', 'diff.bval')],
            'bvec': [('image', 'diff.bvec')],
        })

    return OrderedDict(attach_functions[wf_name]), wf_params, files_crumb_args


def cobre_crumb_workflow(wf_name, data_crumb, output_dir, cache_dir='', config_file='', params=None):
    """ Returns a workflow for the COBRE database.

    Parameters
    ----------
    wf_name: str
        A name for the workflow.
        Choices: 'spm_anat_preproc': MPRAGE preprocessing with SPM12
                 'spm_rest_preproc': MPRAGE+rs-fMRI preprocessing with SPM12

    data_crumb: hansel.Crumb
        The crumb until the subject files.
        Example: Crumb('/home/hansel/cobre/raw/{subject_id}/session_1/{modality}/{image})
        The last 2 crumb arguments of `data_crumb` must be '{modality}/{image}', which indicates each of the
        subject/session files. This argument will be replaced by the corresponding image name.

    cache_dir: str
        The working directory of the workflow.

    output_dir: str
        The output folder path

    config_file: str
        Path to a configuration file. Will use anything compatible with Kaptan.
        Have a look at config.py.

    params: dict with arguments
        crumb_replaces

        atlas_file

    Returns
    -------
    wf: Nipype Workflow
    """
    attach_funcs, cfg_params, file_templates = _cobre_wf_setup(wf_name)

    if params is None:
        params = {}

    if config_file:
        update_config(config_file)

    if params:
        update_config(params)

    if cfg_params is not None:
        update_config(cfg_params)

    wf = build_crumb_workflow(
        attach_funcs,
        data_crumb=data_crumb,
        in_out_kwargs=file_templates,
        output_dir=output_dir,
        cache_dir=cache_dir,
    )

    return wf


def clinical_crumb_workflow(wf_name, data_crumb, output_dir, cache_dir='', config_file='', params=None):
    """ Returns a workflow for the a clinical database.

    Parameters
    ----------
    wf_name: str
        A name for the workflow to be created.
        Choices: 'spm_anat_preproc':     MPRAGE preprocessing with SPM12
                 'spm_anat_pet_preproc': MPRAGE+FDG-PET preprocessing with SPM12
                 'spm_pet_preproc':      FDG-PET only preprocessing with SPM12

    data_crumb: hansel.Crumb
        The crumb until the subject files.
        Example: Crumb('/home/hansel/data/{subject_id}/{session_id}/{modality}/{image})
        The last crumb argument of `data_crumb` must be '{image}', which indicates each of the
        subject/session files. This argument will be replaced by the corresponding image name.

    cache_dir: str
        The working directory of the workflow.

    output_dir: str
        The output folder path

    config_file: str
        Path to a configuration file. Will use anything compatible with Kaptan.
        Have a look at config.py.

    params: dict with arguments
        crumb_replaces

        atlas_file

        raise_on_filenotfound

    Returns
    -------
    wf: Nipype Workflow
    """
    attach_funcs, cfg_params, file_templates = _clinical_wf_setup(wf_name)

    if params is None:
        params = {}

    if config_file:
        update_config(config_file)

    if params:
        update_config(params)

    if cfg_params is not None:
        update_config(cfg_params)

    wf = build_crumb_workflow(
        attach_funcs,
        data_crumb=data_crumb,
        in_out_kwargs=file_templates,
        output_dir=output_dir,
        cache_dir=cache_dir,
    )

    return wf

# -*- coding: utf-8 -*-
"""
Functions to create pipelines for public and not so public available datasets.
"""

from collections import OrderedDict

from neuro_pypes.io import build_crumb_workflow
from neuro_pypes.config import update_config
from neuro_pypes.anat import (
    attach_spm_anat_preprocessing,
    attach_ants_cortical_thickness
)
from neuro_pypes.dmri import (
    attach_spm_fsl_dti_preprocessing,
    attach_camino_tractography
)
from neuro_pypes.fmri import (
    attach_rest_preprocessing,
    attach_rest_grptemplate_preprocessing
)
from neuro_pypes.pet import (
    attach_spm_mrpet_preprocessing,
    attach_spm_pet_preprocessing,
    attach_spm_pet_grouptemplate
)


def _cobre_wf_setup(wf_name):
    """ Return a list of workflow-attach functions and a dict with kwargs for
    the `in_out_crumb_wf` function to run workflows against the COBRE database.

    Parameters
    ----------
    wf_name

    Returns
    -------
    wf_attachers: dict with wf attacher functions

    wf_params: dict with configuration parameters for the workflows.
        Use this only to fixed configurations needed for the correct functioning of the workflows.

    files_crumb_args: dict with kwargs
        This arguments are for the in_out_crumb_wf.
        A dict that declares the values each file type the crumb arguments in `data_crumb` must be replaced with.
        Example:
              {'anat':  [('modality', 'anat_1'),
                         ('image',    'mprage.nii.gz')],
              'rest':   [('modality', 'rest_1'),
                         ('image',    'rest.nii.gz')],
              }
    """
    attach_functions = {
        "spm_anat_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing)
        ],

        "spm_anat_rest_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_rest_preproc", attach_rest_preprocessing),
        ],
    }

    if wf_name not in attach_functions:
        raise KeyError('Expected an existing pipeline name, got {}. '
                       'Available options: {}'.format(wf_name, list(attach_functions.keys())))

    files_crumb_args = {
        'anat': [('modality', 'anat_1'),
                 ('image', 'mprage.nii.gz')]
    }  # 'anat_1/mprage.nii.gz',

    if 'rest' in wf_name:
        files_crumb_args.update({
            'rest': [('modality', 'rest_1'),
                     ('image', 'rest.nii.gz')
                     ],  # 'rest_1/rest.nii.gz'},
        })

    params = {'file_templates': files_crumb_args}

    return OrderedDict(attach_functions[wf_name]), params


def _clinical_wf_setup(wf_name):
    """ Return a list of workflow-attach functions and a dict with kwargs for
    the `in_out_crumb_wf` function to run workflows against the clinical database.

    Parameters
    ----------
    wf_name

    Returns
    -------
    wf_attachers: dict with wf attacher functions

    wf_params: dict with configuration parameters for the workflows.
        Use this only to fixed configurations needed for the correct functioning of the workflows.

    files_crumb_args: dict with kwargs
        This arguments are for the in_out_crumb_wf.
        A dict that declares the values each file type the crumb arguments in `data_crumb` must be replaced with.
        Example:
              {'anat':  [('modality', 'anat_1'),
                         ('image',    'mprage.nii.gz')],
              'rest':   [('modality', 'rest_1'),
                         ('image',    'rest.nii.gz')],
              }
    """
    # MPRAGE bias-field correction, normalization to MNI, and tissue segmentation
    attach_functions = {
        "spm_anat_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing)
        ],

        # PET normalization to MNI
        "spm_pet_preproc": [
            ("spm_pet_preproc", attach_spm_pet_preprocessing)
        ],

        # will create a PET group template
        "spm_pet_template": [
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
        ],

        # MPRAGE preprocessing, PET MNI group template, PET PVC, and PET normalization to group template
        "spm_anat_pet_tpm_pvc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
        ],

        # MPRAGE preprocessing, PET MNI group template, PET PVC, and rest-fMRI
        "spm_anat_pet_pvc_rest": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
            ("spm_rest_preproc", attach_rest_preprocessing),
        ],

        # MPRAGE preprocessing, PET PVC, and PET normalization to MNI
        "spm_anat_pet_pvc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_mrpet_preproc", attach_spm_mrpet_preprocessing),
        ],

        # MPRAGE preprocessing, rs-fMRI preprocessing and normalization to MNI
        "spm_anat_rest_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_rest_preproc", attach_rest_preprocessing),
        ],

        # MPRAGE preprocessing, DTI preprocessing with FSL
        "fsl_dti_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("fsl_dti_preproc", attach_spm_fsl_dti_preprocessing),
        ],

        # MPRAGE preprocessing, DTI preprocessing with FSL, and tractography with Camino
        "anat_dti_camino": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("fsl_dti_preproc", attach_spm_fsl_dti_preprocessing),
            ("camino_tract", attach_camino_tractography),
        ],

        # MPRAGE and PET preprocessing, DTI preprocessing with FSL, and tractography with Camino
        "anat_pet_dti_camino": [("spm_anat_preproc", attach_spm_anat_preprocessing),
                                ("spm_mrpet_preproc", attach_spm_mrpet_preprocessing),
                                ("fsl_dti_preproc", attach_spm_fsl_dti_preprocessing),
                                ("camino_tract", attach_camino_tractography),
                                ],

        # MPRAGE preprocessing, and EPI group template
        "spm_anat_rest_tpm_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_warp_fmri", attach_rest_grptemplate_preprocessing),
        ],

        # MPRAGE preprocessing, EPI and PET group template, and PET and rs-fMRI preprocessing and
        # normalization to group template
        "spm_anat_pet_rest_tpm_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_warp_fmri", attach_rest_grptemplate_preprocessing),
            ("spm_pet_preproc", attach_spm_pet_preprocessing),
            ("spm_pet_grouptemplate", attach_spm_pet_grouptemplate),
        ],

        # MPRAGE preprocessing, EPI group template, and rs-fMRI preprocessing and normalization to MNI
        "spm_anat_pet_rest_preproc": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("spm_rest_preproc", attach_rest_preprocessing),
            ("spm_pet_preproc", attach_spm_mrpet_preprocessing),
        ],

        # MPRAGE and cortical thickness
        "spm_anat_ants_cortical_thick": [
            ("spm_anat_preproc", attach_spm_anat_preprocessing),
            ("ants_cort_thick", attach_ants_cortical_thickness),
        ],
    }

    parameters = {
        "spm_pet_template": [('spm_pet_template.do_petpvc', False), ],
        "spm_anat_pet_tpm_pvc": [('spm_pet_template.do_petpvc', True), ],
    }

    if wf_name not in attach_functions:
        raise KeyError('Expected an existing pipeline name, got {}. '
                       'Available options: {}'.format(wf_name, list(attach_functions.keys())))

    # the pipeline parameters
    wf_params = parameters.get(wf_name, None)
    if wf_params is not None:
        wf_params = dict(wf_params)

    # the input files crumb patterns
    files_crumb_args = {}
    files_crumb_args.update({'anat': [('image', 'anat_hc.nii.gz')]})

    if 'pet' in wf_name:
        files_crumb_args.update({'pet': [('image', 'pet_fdg.nii.gz')], })

    if 'rest' in wf_name:
        files_crumb_args.update({'rest': [('image', 'rest.nii.gz')], })

    if 'dti' in wf_name:
        files_crumb_args.update({
            'diff': [('image', 'diff.nii.gz')],
            'bval': [('image', 'diff.bval')],
            'bvec': [('image', 'diff.bvec')],
        })

    return OrderedDict(attach_functions[wf_name]), wf_params, files_crumb_args


def cobre_crumb_workflow(wf_name, data_crumb, output_dir, cache_dir='', config_file='', params=None):
    """ Returns a workflow for the COBRE database.

    Parameters
    ----------
    wf_name: str
        A name for the workflow.
        Choices: 'spm_anat_preproc': MPRAGE preprocessing with SPM12
                 'spm_rest_preproc': MPRAGE+rs-fMRI preprocessing with SPM12

    data_crumb: hansel.Crumb
        The crumb until the subject files.
        Example: Crumb('/home/hansel/cobre/raw/{subject_id}/session_1/{modality}/{image})
        The last 2 crumb arguments of `data_crumb` must be '{modality}/{image}', which indicates each of the
        subject/session files. This argument will be replaced by the corresponding image name.

    cache_dir: str
        The working directory of the workflow.

    output_dir: str
        The output folder path

    config_file: str
        Path to a configuration file. Will use anything compatible with Kaptan.
        Have a look at config.py.

    params: dict with arguments
        crumb_replaces

        atlas_file

    Returns
    -------
    wf: Nipype Workflow
    """
    attach_funcs, cfg_params, file_templates = _cobre_wf_setup(wf_name)

    if params is None:
        params = {}

    if config_file:
        update_config(config_file)

    if params:
        update_config(params)

    if cfg_params is not None:
        update_config(cfg_params)

    wf = build_crumb_workflow(
        attach_funcs,
        data_crumb=data_crumb,
        in_out_kwargs=file_templates,
        output_dir=output_dir,
        cache_dir=cache_dir,
    )

    return wf


def clinical_crumb_workflow(wf_name, data_crumb, output_dir, cache_dir='', config_file='', params=None):
    """ Returns a workflow for the a clinical database.

    Parameters
    ----------
    wf_name: str
        A name for the workflow to be created.
        Choices: 'spm_anat_preproc':     MPRAGE preprocessing with SPM12
                 'spm_anat_pet_preproc': MPRAGE+FDG-PET preprocessing with SPM12
                 'spm_pet_preproc':      FDG-PET only preprocessing with SPM12

    data_crumb: hansel.Crumb
        The crumb until the subject files.
        Example: Crumb('/home/hansel/data/{subject_id}/{session_id}/{modality}/{image})
        The last crumb argument of `data_crumb` must be '{image}', which indicates each of the
        subject/session files. This argument will be replaced by the corresponding image name.

    cache_dir: str
        The working directory of the workflow.

    output_dir: str
        The output folder path

    config_file: str
        Path to a configuration file. Will use anything compatible with Kaptan.
        Have a look at config.py.

    params: dict with arguments
        crumb_replaces

        atlas_file

        raise_on_filenotfound

    Returns
    -------
    wf: Nipype Workflow
    """
    attach_funcs, cfg_params, file_templates = _clinical_wf_setup(wf_name)

    if params is None:
        params = {}

    if config_file:
        update_config(config_file)

    if params:
        update_config(params)

    if cfg_params is not None:
        update_config(cfg_params)

    wf = build_crumb_workflow(
        attach_funcs,
        data_crumb=data_crumb,
        in_out_kwargs=file_templates,
        output_dir=output_dir,
        cache_dir=cache_dir,
    )

    return wf
# -*- coding: utf-8 -*- Functions to create pipelines for public and not so public available datasets. Return a list of workflow-attach functions and a dict with kwargs for     the `in_out_crumb_wf` function to run workflows against the COBRE database.      Parameters     ----------     wf_name      Returns     -------     wf_attachers: dict with wf attacher functions      wf_params: dict with configuration parameters for the workflows.         Use this only to fixed configurations needed for the correct functioning of the workflows.      files_crumb_args: dict with kwargs         This arguments are for the in_out_crumb_wf.         A dict that declares the values each file type the crumb arguments in `data_crumb` must be replaced with.         Example:               {'anat':  [('modality', 'anat_1'),                          ('image',    'mprage.nii.gz')],               'rest':   [('modality', 'rest_1'),                          ('image',    'rest.nii.gz')],               } # 'anat_1/mprage.nii.gz', # 'rest_1/rest.nii.gz'}, Return a list of workflow-attach functions and a dict with kwargs for     the `in_out_crumb_wf` function to run workflows against the clinical database.      Parameters     ----------     wf_name      Returns     -------     wf_attachers: dict with wf attacher functions      wf_params: dict with configuration parameters for the workflows.         Use this only to fixed configurations needed for the correct functioning of the workflows.      files_crumb_args: dict with kwargs         This arguments are for the in_out_crumb_wf.         A dict that declares the values each file type the crumb arguments in `data_crumb` must be replaced with.         Example:               {'anat':  [('modality', 'anat_1'),                          ('image',    'mprage.nii.gz')],               'rest':   [('modality', 'rest_1'),                          ('image',    'rest.nii.gz')],               } # MPRAGE bias-field correction, normalization to MNI, and tissue segmentation # PET normalization to MNI # will create a PET group template # MPRAGE preprocessing, PET MNI group template, PET PVC, and PET normalization to group template # MPRAGE preprocessing, PET MNI group template, PET PVC, and rest-fMRI # MPRAGE preprocessing, PET PVC, and PET normalization to MNI # MPRAGE preprocessing, rs-fMRI preprocessing and normalization to MNI # MPRAGE preprocessing, DTI preprocessing with FSL # MPRAGE preprocessing, DTI preprocessing with FSL, and tractography with Camino # MPRAGE and PET preprocessing, DTI preprocessing with FSL, and tractography with Camino # MPRAGE preprocessing, and EPI group template # MPRAGE preprocessing, EPI and PET group template, and PET and rs-fMRI preprocessing and # normalization to group template # MPRAGE preprocessing, EPI group template, and rs-fMRI preprocessing and normalization to MNI # MPRAGE and cortical thickness # the pipeline parameters # the input files crumb patterns Returns a workflow for the COBRE database.      Parameters     ----------     wf_name: str         A name for the workflow.         Choices: 'spm_anat_preproc': MPRAGE preprocessing with SPM12                  'spm_rest_preproc': MPRAGE+rs-fMRI preprocessing with SPM12      data_crumb: hansel.Crumb         The crumb until the subject files.         Example: Crumb('/home/hansel/cobre/raw/{subject_id}/session_1/{modality}/{image})         The last 2 crumb arguments of `data_crumb` must be '{modality}/{image}', which indicates each of the         subject/session files. This argument will be replaced by the corresponding image name.      cache_dir: str         The working directory of the workflow.      output_dir: str         The output folder path      config_file: str         Path to a configuration file. Will use anything compatible with Kaptan.         Have a look at config.py.      params: dict with arguments         crumb_replaces          atlas_file      Returns     -------     wf: Nipype Workflow Returns a workflow for the a clinical database.      Parameters     ----------     wf_name: str         A name for the workflow to be created.         Choices: 'spm_anat_preproc':     MPRAGE preprocessing with SPM12                  'spm_anat_pet_preproc': MPRAGE+FDG-PET preprocessing with SPM12                  'spm_pet_preproc':      FDG-PET only preprocessing with SPM12      data_crumb: hansel.Crumb         The crumb until the subject files.         Example: Crumb('/home/hansel/data/{subject_id}/{session_id}/{modality}/{image})         The last crumb argument of `data_crumb` must be '{image}', which indicates each of the         subject/session files. This argument will be replaced by the corresponding image name.      cache_dir: str         The working directory of the workflow.      output_dir: str         The output folder path      config_file: str         Path to a configuration file. Will use anything compatible with Kaptan.         Have a look at config.py.      params: dict with arguments         crumb_replaces          atlas_file          raise_on_filenotfound      Returns     -------     wf: Nipype Workflow