rsfmri_vol_surface_preprocessing.py

#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
====================================
rsfMRI: ANTS, FS, FSL, SPM, aCompCor
====================================


A preprocessing workflow for Siemens resting state data.

This workflow makes use of:

- ANTS
- FreeSurfer
- FSL
- SPM
- CompCor

For example::

  python rsfmri_preprocessing.py -d /data/12345-34-1.dcm -f /data/Resting.nii
      -s subj001 -o output -p PBS --plugin_args "dict(qsub_args='-q many')"

  or

  python rsfmri_vol_surface_preprocessing.py -f SUB_1024011/E?/func/rest.nii
      -t OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz --TR 2 -s SUB_1024011
      --subjects_dir fsdata --slice_times 0 17 1 18 2 19 3 20 4 21 5 22 6 23
      7 24 8 25 9 26 10 27 11 28 12 29 13 30 14 31 15 32 16 -o .

This workflow takes resting timeseries and a Siemens dicom file corresponding
to it and preprocesses it to produce timeseries coordinates or grayordinates.

This workflow also requires 2mm subcortical atlas and templates that are
available from:

http://mindboggle.info/data.html

specifically the 2mm versions of:

- `Joint Fusion Atlas <http://mindboggle.info/data/atlases/jointfusion/OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_2mm_v2.nii.gz>`_
- `MNI template <http://mindboggle.info/data/templates/ants/OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz>`_
"""

from __future__ import division, unicode_literals
from builtins import open, range, str

import os

from nipype.interfaces.base import CommandLine
CommandLine.set_default_terminal_output('allatonce')

from dicom import read_file

from nipype.interfaces import (spm, fsl, Function, ants, freesurfer)
from nipype.interfaces.c3 import C3dAffineTool

fsl.FSLCommand.set_default_output_type('NIFTI')

from nipype import Workflow, Node, MapNode
from nipype.interfaces import matlab as mlab

mlab.MatlabCommand.set_default_matlab_cmd("matlab -nodisplay")
# If SPM is not in your MATLAB path you should add it here
# mlab.MatlabCommand.set_default_paths('/software/matlab/spm12')

from nipype.algorithms.rapidart import ArtifactDetect
from nipype.algorithms.misc import TSNR, CalculateMedian
from nipype.interfaces.utility import Rename, Merge, IdentityInterface
from nipype.utils.filemanip import filename_to_list
from nipype.interfaces.io import DataSink, FreeSurferSource

import numpy as np
import scipy as sp
import nibabel as nb

imports = [
    'import os', 'import nibabel as nb', 'import numpy as np',
    'import scipy as sp',
    'from nipype.utils.filemanip import filename_to_list, list_to_filename, split_filename',
    'from scipy.special import legendre'
]


def get_info(dicom_files):
    from dcmstack.extract import default_extractor
    """Given a Siemens dicom file return metadata

    Returns
    -------
    RepetitionTime
    Slice Acquisition Times
    Spacing between slices
    """
    meta = default_extractor(
        read_file(
            filename_to_list(dicom_files)[0],
            stop_before_pixels=True,
            force=True))
    return (meta['RepetitionTime'] / 1000., meta['CsaImage.MosaicRefAcqTimes'],
            meta['SpacingBetweenSlices'])


def median(in_files):
    """Computes an average of the median of each realigned timeseries

    Parameters
    ----------

    in_files: one or more realigned Nifti 4D time series

    Returns
    -------

    out_file: a 3D Nifti file
    """
    import numpy as np
    import nibabel as nb
    from nipype.utils import NUMPY_MMAP
    average = None
    for idx, filename in enumerate(filename_to_list(in_files)):
        img = nb.load(filename, mmap=NUMPY_MMAP)
        data = np.median(img.get_data(), axis=3)
        if average is None:
            average = data
        else:
            average = average + data
    median_img = nb.Nifti1Image(average / float(idx + 1), img.affine,
                                img.header)
    filename = os.path.join(os.getcwd(), 'median.nii.gz')
    median_img.to_filename(filename)
    return filename


def bandpass_filter(files, lowpass_freq, highpass_freq, fs):
    """Bandpass filter the input files

    Parameters
    ----------
    files: list of 4d nifti files
    lowpass_freq: cutoff frequency for the low pass filter (in Hz)
    highpass_freq: cutoff frequency for the high pass filter (in Hz)
    fs: sampling rate (in Hz)
    """
    from nipype.utils.filemanip import split_filename, list_to_filename
    import numpy as np
    import nibabel as nb
    from nipype.utils import NUMPY_MMAP
    out_files = []
    for filename in filename_to_list(files):
        path, name, ext = split_filename(filename)
        out_file = os.path.join(os.getcwd(), name + '_bp' + ext)
        img = nb.load(filename, mmap=NUMPY_MMAP)
        timepoints = img.shape[-1]
        F = np.zeros((timepoints))
        lowidx = int(timepoints / 2) + 1
        if lowpass_freq > 0:
            lowidx = np.round(lowpass_freq / fs * timepoints)
        highidx = 0
        if highpass_freq > 0:
            highidx = np.round(highpass_freq / fs * timepoints)
        F[highidx:lowidx] = 1
        F = ((F + F[::-1]) > 0).astype(int)
        data = img.get_data()
        if np.all(F == 1):
            filtered_data = data
        else:
            filtered_data = np.real(np.fft.ifftn(np.fft.fftn(data) * F))
        img_out = nb.Nifti1Image(filtered_data, img.affine, img.header)
        img_out.to_filename(out_file)
        out_files.append(out_file)
    return list_to_filename(out_files)


def motion_regressors(motion_params, order=0, derivatives=1):
    """Compute motion regressors upto given order and derivative

    motion + d(motion)/dt + d2(motion)/dt2 (linear + quadratic)
    """
    import numpy as np
    out_files = []
    for idx, filename in enumerate(filename_to_list(motion_params)):
        params = np.genfromtxt(filename)
        out_params = params
        for d in range(1, derivatives + 1):
            cparams = np.vstack((np.repeat(params[0, :][None, :], d, axis=0),
                                 params))
            out_params = np.hstack((out_params, np.diff(cparams, d, axis=0)))
        out_params2 = out_params
        for i in range(2, order + 1):
            out_params2 = np.hstack((out_params2, np.power(out_params, i)))
        filename = os.path.join(os.getcwd(), "motion_regressor%02d.txt" % idx)
        np.savetxt(filename, out_params2, fmt=b"%.10f")
        out_files.append(filename)
    return out_files


def build_filter1(motion_params, comp_norm, outliers, detrend_poly=None):
    """Builds a regressor set comprisong motion parameters, composite norm and
    outliers

    The outliers are added as a single time point column for each outlier


    Parameters
    ----------

    motion_params: a text file containing motion parameters and its derivatives
    comp_norm: a text file containing the composite norm
    outliers: a text file containing 0-based outlier indices
    detrend_poly: number of polynomials to add to detrend

    Returns
    -------
    components_file: a text file containing all the regressors
    """
    import numpy as np
    import nibabel as nb
    from scipy.special import legendre
    out_files = []
    for idx, filename in enumerate(filename_to_list(motion_params)):
        params = np.genfromtxt(filename)
        norm_val = np.genfromtxt(filename_to_list(comp_norm)[idx])
        out_params = np.hstack((params, norm_val[:, None]))
        try:
            outlier_val = np.genfromtxt(filename_to_list(outliers)[idx])
        except IOError:
            outlier_val = np.empty((0))
        for index in np.atleast_1d(outlier_val):
            outlier_vector = np.zeros((out_params.shape[0], 1))
            outlier_vector[index] = 1
            out_params = np.hstack((out_params, outlier_vector))
        if detrend_poly:
            timepoints = out_params.shape[0]
            X = np.empty((timepoints, 0))
            for i in range(detrend_poly):
                X = np.hstack((X, legendre(i + 1)(np.linspace(
                    -1, 1, timepoints))[:, None]))
            out_params = np.hstack((out_params, X))
        filename = os.path.join(os.getcwd(), "filter_regressor%02d.txt" % idx)
        np.savetxt(filename, out_params, fmt=b"%.10f")
        out_files.append(filename)
    return out_files


def extract_noise_components(realigned_file,
                             mask_file,
                             num_components=5,
                             extra_regressors=None):
    """Derive components most reflective of physiological noise

    Parameters
    ----------
    realigned_file: a 4D Nifti file containing realigned volumes
    mask_file: a 3D Nifti file containing white matter + ventricular masks
    num_components: number of components to use for noise decomposition
    extra_regressors: additional regressors to add

    Returns
    -------
    components_file: a text file containing the noise components
    """
    from scipy.linalg.decomp_svd import svd
    import numpy as np
    import nibabel as nb
    from nipype.utils import NUMPY_MMAP
    import os
    imgseries = nb.load(realigned_file, mmap=NUMPY_MMAP)
    components = None
    for filename in filename_to_list(mask_file):
        mask = nb.load(filename, mmap=NUMPY_MMAP).get_data()
        if len(np.nonzero(mask > 0)[0]) == 0:
            continue
        voxel_timecourses = imgseries.get_data()[mask > 0]
        voxel_timecourses[np.isnan(np.sum(voxel_timecourses, axis=1)), :] = 0
        # remove mean and normalize by variance
        # voxel_timecourses.shape == [nvoxels, time]
        X = voxel_timecourses.T
        stdX = np.std(X, axis=0)
        stdX[stdX == 0] = 1.
        stdX[np.isnan(stdX)] = 1.
        stdX[np.isinf(stdX)] = 1.
        X = (X - np.mean(X, axis=0)) / stdX
        u, _, _ = svd(X, full_matrices=False)
        if components is None:
            components = u[:, :num_components]
        else:
            components = np.hstack((components, u[:, :num_components]))
    if extra_regressors:
        regressors = np.genfromtxt(extra_regressors)
        components = np.hstack((components, regressors))
    components_file = os.path.join(os.getcwd(), 'noise_components.txt')
    np.savetxt(components_file, components, fmt=b"%.10f")
    return components_file


def rename(in_files, suffix=None):
    from nipype.utils.filemanip import (filename_to_list, split_filename,
                                        list_to_filename)
    out_files = []
    for idx, filename in enumerate(filename_to_list(in_files)):
        _, name, ext = split_filename(filename)
        if suffix is None:
            out_files.append(name + ('_%03d' % idx) + ext)
        else:
            out_files.append(name + suffix + ext)
    return list_to_filename(out_files)


def get_aparc_aseg(files):
    """Return the aparc+aseg.mgz file"""
    for name in files:
        if 'aparc+aseg.mgz' in name:
            return name
    raise ValueError('aparc+aseg.mgz not found')


def extract_subrois(timeseries_file, label_file, indices):
    """Extract voxel time courses for each subcortical roi index

    Parameters
    ----------

    timeseries_file: a 4D Nifti file
    label_file: a 3D file containing rois in the same space/size of the 4D file
    indices: a list of indices for ROIs to extract.

    Returns
    -------
    out_file: a text file containing time courses for each voxel of each roi
        The first four columns are: freesurfer index, i, j, k positions in the
        label file
    """
    from nipype.utils.filemanip import split_filename
    import nibabel as nb
    from nipype.utils import NUMPY_MMAP
    import os
    img = nb.load(timeseries_file, mmap=NUMPY_MMAP)
    data = img.get_data()
    roiimg = nb.load(label_file, mmap=NUMPY_MMAP)
    rois = roiimg.get_data()
    prefix = split_filename(timeseries_file)[1]
    out_ts_file = os.path.join(os.getcwd(), '%s_subcortical_ts.txt' % prefix)
    with open(out_ts_file, 'wt') as fp:
        for fsindex in indices:
            ijk = np.nonzero(rois == fsindex)
            ts = data[ijk]
            for i0, row in enumerate(ts):
                fp.write('%d,%d,%d,%d,' % (
                    fsindex, ijk[0][i0], ijk[1][i0],
                    ijk[2][i0]) + ','.join(['%.10f' % val
                                            for val in row]) + '\n')
    return out_ts_file


def combine_hemi(left, right):
    """Combine left and right hemisphere time series into a single text file
    """
    import os
    import numpy as np
    from nipype.utils import NUMPY_MMAP
    lh_data = nb.load(left, mmap=NUMPY_MMAP).get_data()
    rh_data = nb.load(right, mmap=NUMPY_MMAP).get_data()

    indices = np.vstack((1000000 + np.arange(0, lh_data.shape[0])[:, None],
                         2000000 + np.arange(0, rh_data.shape[0])[:, None]))
    all_data = np.hstack((indices,
                          np.vstack((lh_data.squeeze(), rh_data.squeeze()))))
    filename = left.split('.')[1] + '_combined.txt'
    np.savetxt(
        filename,
        all_data,
        fmt=','.join(['%d'] + ['%.10f'] * (all_data.shape[1] - 1)))
    return os.path.abspath(filename)


def create_reg_workflow(name='registration'):
    """Create a FEAT preprocessing workflow together with freesurfer

    Parameters
    ----------

        name : name of workflow (default: 'registration')

    Inputs::

        inputspec.source_files : files (filename or list of filenames to register)
        inputspec.mean_image : reference image to use
        inputspec.anatomical_image : anatomical image to coregister to
        inputspec.target_image : registration target

    Outputs::

        outputspec.func2anat_transform : FLIRT transform
        outputspec.anat2target_transform : FLIRT+FNIRT transform
        outputspec.transformed_files : transformed files in target space
        outputspec.transformed_mean : mean image in target space
    """

    register = Workflow(name=name)

    inputnode = Node(
        interface=IdentityInterface(fields=[
            'source_files', 'mean_image', 'subject_id', 'subjects_dir',
            'target_image'
        ]),
        name='inputspec')

    outputnode = Node(
        interface=IdentityInterface(fields=[
            'func2anat_transform', 'out_reg_file', 'anat2target_transform',
            'transforms', 'transformed_mean', 'segmentation_files',
            'anat2target', 'aparc'
        ]),
        name='outputspec')

    # Get the subject's freesurfer source directory
    fssource = Node(FreeSurferSource(), name='fssource')
    fssource.run_without_submitting = True
    register.connect(inputnode, 'subject_id', fssource, 'subject_id')
    register.connect(inputnode, 'subjects_dir', fssource, 'subjects_dir')

    convert = Node(freesurfer.MRIConvert(out_type='nii'), name="convert")
    register.connect(fssource, 'T1', convert, 'in_file')

    # Coregister the median to the surface
    bbregister = Node(freesurfer.BBRegister(), name='bbregister')
    bbregister.inputs.init = 'fsl'
    bbregister.inputs.contrast_type = 't2'
    bbregister.inputs.out_fsl_file = True
    bbregister.inputs.epi_mask = True
    register.connect(inputnode, 'subject_id', bbregister, 'subject_id')
    register.connect(inputnode, 'mean_image', bbregister, 'source_file')
    register.connect(inputnode, 'subjects_dir', bbregister, 'subjects_dir')
    """
    Estimate the tissue classes from the anatomical image. But use spm's segment
    as FSL appears to be breaking.
    """

    stripper = Node(fsl.BET(), name='stripper')
    register.connect(convert, 'out_file', stripper, 'in_file')
    fast = Node(fsl.FAST(), name='fast')
    register.connect(stripper, 'out_file', fast, 'in_files')
    """
    Binarize the segmentation
    """

    binarize = MapNode(
        fsl.ImageMaths(op_string='-nan -thr 0.9 -ero -bin'),
        iterfield=['in_file'],
        name='binarize')
    register.connect(fast, 'partial_volume_files', binarize, 'in_file')
    """
    Apply inverse transform to take segmentations to functional space
    """

    applyxfm = MapNode(
        freesurfer.ApplyVolTransform(inverse=True, interp='nearest'),
        iterfield=['target_file'],
        name='inverse_transform')
    register.connect(inputnode, 'subjects_dir', applyxfm, 'subjects_dir')
    register.connect(bbregister, 'out_reg_file', applyxfm, 'reg_file')
    register.connect(binarize, 'out_file', applyxfm, 'target_file')
    register.connect(inputnode, 'mean_image', applyxfm, 'source_file')
    """
    Apply inverse transform to aparc file
    """

    aparcxfm = Node(
        freesurfer.ApplyVolTransform(inverse=True, interp='nearest'),
        name='aparc_inverse_transform')
    register.connect(inputnode, 'subjects_dir', aparcxfm, 'subjects_dir')
    register.connect(bbregister, 'out_reg_file', aparcxfm, 'reg_file')
    register.connect(fssource, ('aparc_aseg', get_aparc_aseg), aparcxfm,
                     'target_file')
    register.connect(inputnode, 'mean_image', aparcxfm, 'source_file')
    """
    Convert the BBRegister transformation to ANTS ITK format
    """

    convert2itk = Node(C3dAffineTool(), name='convert2itk')
    convert2itk.inputs.fsl2ras = True
    convert2itk.inputs.itk_transform = True
    register.connect(bbregister, 'out_fsl_file', convert2itk, 'transform_file')
    register.connect(inputnode, 'mean_image', convert2itk, 'source_file')
    register.connect(stripper, 'out_file', convert2itk, 'reference_file')
    """
    Compute registration between the subject's structural and MNI template
    This is currently set to perform a very quick registration. However, the
    registration can be made significantly more accurate for cortical
    structures by increasing the number of iterations
    All parameters are set using the example from:
    #https://github.com/stnava/ANTs/blob/master/Scripts/newAntsExample.sh
    """

    reg = Node(ants.Registration(), name='antsRegister')
    reg.inputs.output_transform_prefix = "output_"
    reg.inputs.transforms = ['Rigid', 'Affine', 'SyN']
    reg.inputs.transform_parameters = [(0.1, ), (0.1, ), (0.2, 3.0, 0.0)]
    reg.inputs.number_of_iterations = [[10000, 11110, 11110]] * 2 + [[
        100, 30, 20
    ]]
    reg.inputs.dimension = 3
    reg.inputs.write_composite_transform = True
    reg.inputs.collapse_output_transforms = True
    reg.inputs.initial_moving_transform_com = True
    reg.inputs.metric = ['Mattes'] * 2 + [['Mattes', 'CC']]
    reg.inputs.metric_weight = [1] * 2 + [[0.5, 0.5]]
    reg.inputs.radius_or_number_of_bins = [32] * 2 + [[32, 4]]
    reg.inputs.sampling_strategy = ['Regular'] * 2 + [[None, None]]
    reg.inputs.sampling_percentage = [0.3] * 2 + [[None, None]]
    reg.inputs.convergence_threshold = [1.e-8] * 2 + [-0.01]
    reg.inputs.convergence_window_size = [20] * 2 + [5]
    reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]]
    reg.inputs.sigma_units = ['vox'] * 3
    reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]]
    reg.inputs.use_estimate_learning_rate_once = [True] * 3
    reg.inputs.use_histogram_matching = [False] * 2 + [True]
    reg.inputs.winsorize_lower_quantile = 0.005
    reg.inputs.winsorize_upper_quantile = 0.995
    reg.inputs.float = True
    reg.inputs.output_warped_image = 'output_warped_image.nii.gz'
    reg.inputs.num_threads = 4
    reg.plugin_args = {'qsub_args': '-l nodes=1:ppn=4'}
    register.connect(stripper, 'out_file', reg, 'moving_image')
    register.connect(inputnode, 'target_image', reg, 'fixed_image')
    """
    Concatenate the affine and ants transforms into a list
    """

    merge = Node(Merge(2), iterfield=['in2'], name='mergexfm')
    register.connect(convert2itk, 'itk_transform', merge, 'in2')
    register.connect(reg, 'composite_transform', merge, 'in1')
    """
    Transform the mean image. First to anatomical and then to target
    """

    warpmean = Node(ants.ApplyTransforms(), name='warpmean')
    warpmean.inputs.input_image_type = 3
    warpmean.inputs.interpolation = 'Linear'
    warpmean.inputs.invert_transform_flags = [False, False]
    warpmean.terminal_output = 'file'
    warpmean.inputs.args = '--float'
    warpmean.inputs.num_threads = 4

    register.connect(inputnode, 'target_image', warpmean, 'reference_image')
    register.connect(inputnode, 'mean_image', warpmean, 'input_image')
    register.connect(merge, 'out', warpmean, 'transforms')
    """
    Assign all the output files
    """

    register.connect(reg, 'warped_image', outputnode, 'anat2target')
    register.connect(warpmean, 'output_image', outputnode, 'transformed_mean')
    register.connect(applyxfm, 'transformed_file', outputnode,
                     'segmentation_files')
    register.connect(aparcxfm, 'transformed_file', outputnode, 'aparc')
    register.connect(bbregister, 'out_fsl_file', outputnode,
                     'func2anat_transform')
    register.connect(bbregister, 'out_reg_file', outputnode, 'out_reg_file')
    register.connect(reg, 'composite_transform', outputnode,
                     'anat2target_transform')
    register.connect(merge, 'out', outputnode, 'transforms')

    return register


"""
Creates the main preprocessing workflow
"""


def create_workflow(files,
                    target_file,
                    subject_id,
                    TR,
                    slice_times,
                    norm_threshold=1,
                    num_components=5,
                    vol_fwhm=None,
                    surf_fwhm=None,
                    lowpass_freq=-1,
                    highpass_freq=-1,
                    subjects_dir=None,
                    sink_directory=os.getcwd(),
                    target_subject=['fsaverage3', 'fsaverage4'],
                    name='resting'):

    wf = Workflow(name=name)

    # Rename files in case they are named identically
    name_unique = MapNode(
        Rename(format_string='rest_%(run)02d'),
        iterfield=['in_file', 'run'],
        name='rename')
    name_unique.inputs.keep_ext = True
    name_unique.inputs.run = list(range(1, len(files) + 1))
    name_unique.inputs.in_file = files

    realign = Node(interface=spm.Realign(), name="realign")
    realign.inputs.jobtype = 'estwrite'

    num_slices = len(slice_times)
    slice_timing = Node(interface=spm.SliceTiming(), name="slice_timing")
    slice_timing.inputs.num_slices = num_slices
    slice_timing.inputs.time_repetition = TR
    slice_timing.inputs.time_acquisition = TR - TR / float(num_slices)
    slice_timing.inputs.slice_order = (np.argsort(slice_times) + 1).tolist()
    slice_timing.inputs.ref_slice = int(num_slices / 2)

    # Comute TSNR on realigned data regressing polynomials upto order 2
    tsnr = MapNode(TSNR(regress_poly=2), iterfield=['in_file'], name='tsnr')
    wf.connect(slice_timing, 'timecorrected_files', tsnr, 'in_file')

    # Compute the median image across runs
    calc_median = Node(CalculateMedian(), name='median')
    wf.connect(tsnr, 'detrended_file', calc_median, 'in_files')
    """Segment and Register
    """

    registration = create_reg_workflow(name='registration')
    wf.connect(calc_median, 'median_file', registration,
               'inputspec.mean_image')
    registration.inputs.inputspec.subject_id = subject_id
    registration.inputs.inputspec.subjects_dir = subjects_dir
    registration.inputs.inputspec.target_image = target_file
    """Use :class:`nipype.algorithms.rapidart` to determine which of the
    images in the functional series are outliers based on deviations in
    intensity or movement.
    """

    art = Node(interface=ArtifactDetect(), name="art")
    art.inputs.use_differences = [True, True]
    art.inputs.use_norm = True
    art.inputs.norm_threshold = norm_threshold
    art.inputs.zintensity_threshold = 9
    art.inputs.mask_type = 'spm_global'
    art.inputs.parameter_source = 'SPM'
    """Here we are connecting all the nodes together. Notice that we add the merge node only if you choose
    to use 4D. Also `get_vox_dims` function is passed along the input volume of normalise to set the optimal
    voxel sizes.
    """

    wf.connect([
        (name_unique, realign, [('out_file', 'in_files')]),
        (realign, slice_timing, [('realigned_files', 'in_files')]),
        (slice_timing, art, [('timecorrected_files', 'realigned_files')]),
        (realign, art, [('realignment_parameters', 'realignment_parameters')]),
    ])

    def selectindex(files, idx):
        import numpy as np
        from nipype.utils.filemanip import filename_to_list, list_to_filename
        return list_to_filename(
            np.array(filename_to_list(files))[idx].tolist())

    mask = Node(fsl.BET(), name='getmask')
    mask.inputs.mask = True
    wf.connect(calc_median, 'median_file', mask, 'in_file')

    # get segmentation in normalized functional space

    def merge_files(in1, in2):
        out_files = filename_to_list(in1)
        out_files.extend(filename_to_list(in2))
        return out_files

    # filter some noise

    # Compute motion regressors
    motreg = Node(
        Function(
            input_names=['motion_params', 'order', 'derivatives'],
            output_names=['out_files'],
            function=motion_regressors,
            imports=imports),
        name='getmotionregress')
    wf.connect(realign, 'realignment_parameters', motreg, 'motion_params')

    # Create a filter to remove motion and art confounds
    createfilter1 = Node(
        Function(
            input_names=[
                'motion_params', 'comp_norm', 'outliers', 'detrend_poly'
            ],
            output_names=['out_files'],
            function=build_filter1,
            imports=imports),
        name='makemotionbasedfilter')
    createfilter1.inputs.detrend_poly = 2
    wf.connect(motreg, 'out_files', createfilter1, 'motion_params')
    wf.connect(art, 'norm_files', createfilter1, 'comp_norm')
    wf.connect(art, 'outlier_files', createfilter1, 'outliers')

    filter1 = MapNode(
        fsl.GLM(
            out_f_name='F_mcart.nii', out_pf_name='pF_mcart.nii', demean=True),
        iterfield=['in_file', 'design', 'out_res_name'],
        name='filtermotion')

    wf.connect(slice_timing, 'timecorrected_files', filter1, 'in_file')
    wf.connect(slice_timing, ('timecorrected_files', rename, '_filtermotart'),
               filter1, 'out_res_name')
    wf.connect(createfilter1, 'out_files', filter1, 'design')

    createfilter2 = MapNode(
        Function(
            input_names=[
                'realigned_file', 'mask_file', 'num_components',
                'extra_regressors'
            ],
            output_names=['out_files'],
            function=extract_noise_components,
            imports=imports),
        iterfield=['realigned_file', 'extra_regressors'],
        name='makecompcorrfilter')
    createfilter2.inputs.num_components = num_components

    wf.connect(createfilter1, 'out_files', createfilter2, 'extra_regressors')
    wf.connect(filter1, 'out_res', createfilter2, 'realigned_file')
    wf.connect(registration,
               ('outputspec.segmentation_files', selectindex, [0, 2]),
               createfilter2, 'mask_file')

    filter2 = MapNode(
        fsl.GLM(out_f_name='F.nii', out_pf_name='pF.nii', demean=True),
        iterfield=['in_file', 'design', 'out_res_name'],
        name='filter_noise_nosmooth')
    wf.connect(filter1, 'out_res', filter2, 'in_file')
    wf.connect(filter1, ('out_res', rename, '_cleaned'), filter2,
               'out_res_name')
    wf.connect(createfilter2, 'out_files', filter2, 'design')
    wf.connect(mask, 'mask_file', filter2, 'mask')

    bandpass = Node(
        Function(
            input_names=['files', 'lowpass_freq', 'highpass_freq', 'fs'],
            output_names=['out_files'],
            function=bandpass_filter,
            imports=imports),
        name='bandpass_unsmooth')
    bandpass.inputs.fs = 1. / TR
    bandpass.inputs.highpass_freq = highpass_freq
    bandpass.inputs.lowpass_freq = lowpass_freq
    wf.connect(filter2, 'out_res', bandpass, 'files')
    """Smooth the functional data using
    :class:`nipype.interfaces.spm.Smooth`.
    """

    smooth = Node(interface=spm.Smooth(), name="smooth")
    smooth.inputs.fwhm = vol_fwhm

    wf.connect(bandpass, 'out_files', smooth, 'in_files')

    collector = Node(Merge(2), name='collect_streams')
    wf.connect(smooth, 'smoothed_files', collector, 'in1')
    wf.connect(bandpass, 'out_files', collector, 'in2')
    """
    Transform the remaining images. First to anatomical and then to target
    """

    warpall = MapNode(
        ants.ApplyTransforms(), iterfield=['input_image'], name='warpall')
    warpall.inputs.input_image_type = 3
    warpall.inputs.interpolation = 'Linear'
    warpall.inputs.invert_transform_flags = [False, False]
    warpall.terminal_output = 'file'
    warpall.inputs.reference_image = target_file
    warpall.inputs.args = '--float'
    warpall.inputs.num_threads = 1

    # transform to target
    wf.connect(collector, 'out', warpall, 'input_image')
    wf.connect(registration, 'outputspec.transforms', warpall, 'transforms')

    mask_target = Node(fsl.ImageMaths(op_string='-bin'), name='target_mask')

    wf.connect(registration, 'outputspec.anat2target', mask_target, 'in_file')

    maskts = MapNode(fsl.ApplyMask(), iterfield=['in_file'], name='ts_masker')
    wf.connect(warpall, 'output_image', maskts, 'in_file')
    wf.connect(mask_target, 'out_file', maskts, 'mask_file')

    # map to surface
    # extract aparc+aseg ROIs
    # extract subcortical ROIs
    # extract target space ROIs
    # combine subcortical and cortical rois into a single cifti file

    #######
    # Convert aparc to subject functional space

    # Sample the average time series in aparc ROIs
    sampleaparc = MapNode(
        freesurfer.SegStats(default_color_table=True),
        iterfield=['in_file', 'summary_file', 'avgwf_txt_file'],
        name='aparc_ts')
    sampleaparc.inputs.segment_id = (
        [8] + list(range(10, 14)) + [17, 18, 26, 47] + list(range(49, 55)) +
        [58] + list(range(1001, 1036)) + list(range(2001, 2036)))

    wf.connect(registration, 'outputspec.aparc', sampleaparc,
               'segmentation_file')
    wf.connect(collector, 'out', sampleaparc, 'in_file')

    def get_names(files, suffix):
        """Generate appropriate names for output files
        """
        from nipype.utils.filemanip import (split_filename, filename_to_list,
                                            list_to_filename)
        out_names = []
        for filename in files:
            _, name, _ = split_filename(filename)
            out_names.append(name + suffix)
        return list_to_filename(out_names)

    wf.connect(collector, ('out', get_names, '_avgwf.txt'), sampleaparc,
               'avgwf_txt_file')
    wf.connect(collector, ('out', get_names, '_summary.stats'), sampleaparc,
               'summary_file')

    # Sample the time series onto the surface of the target surface. Performs
    # sampling into left and right hemisphere
    target = Node(IdentityInterface(fields=['target_subject']), name='target')
    target.iterables = ('target_subject', filename_to_list(target_subject))

    samplerlh = MapNode(
        freesurfer.SampleToSurface(),
        iterfield=['source_file'],
        name='sampler_lh')
    samplerlh.inputs.sampling_method = "average"
    samplerlh.inputs.sampling_range = (0.1, 0.9, 0.1)
    samplerlh.inputs.sampling_units = "frac"
    samplerlh.inputs.interp_method = "trilinear"
    samplerlh.inputs.smooth_surf = surf_fwhm
    # samplerlh.inputs.cortex_mask = True
    samplerlh.inputs.out_type = 'niigz'
    samplerlh.inputs.subjects_dir = subjects_dir

    samplerrh = samplerlh.clone('sampler_rh')

    samplerlh.inputs.hemi = 'lh'
    wf.connect(collector, 'out', samplerlh, 'source_file')
    wf.connect(registration, 'outputspec.out_reg_file', samplerlh, 'reg_file')
    wf.connect(target, 'target_subject', samplerlh, 'target_subject')

    samplerrh.set_input('hemi', 'rh')
    wf.connect(collector, 'out', samplerrh, 'source_file')
    wf.connect(registration, 'outputspec.out_reg_file', samplerrh, 'reg_file')
    wf.connect(target, 'target_subject', samplerrh, 'target_subject')

    # Combine left and right hemisphere to text file
    combiner = MapNode(
        Function(
            input_names=['left', 'right'],
            output_names=['out_file'],
            function=combine_hemi,
            imports=imports),
        iterfield=['left', 'right'],
        name="combiner")
    wf.connect(samplerlh, 'out_file', combiner, 'left')
    wf.connect(samplerrh, 'out_file', combiner, 'right')

    # Sample the time series file for each subcortical roi
    ts2txt = MapNode(
        Function(
            input_names=['timeseries_file', 'label_file', 'indices'],
            output_names=['out_file'],
            function=extract_subrois,
            imports=imports),
        iterfield=['timeseries_file'],
        name='getsubcortts')
    ts2txt.inputs.indices = [8] + list(range(10, 14)) + [17, 18, 26, 47] +\
        list(range(49, 55)) + [58]
    ts2txt.inputs.label_file = \
        os.path.abspath(('OASIS-TRT-20_jointfusion_DKT31_CMA_labels_in_MNI152_'
                         '2mm_v2.nii.gz'))
    wf.connect(maskts, 'out_file', ts2txt, 'timeseries_file')

    ######

    substitutions = [('_target_subject_',
                      ''), ('_filtermotart_cleaned_bp_trans_masked', ''),
                     ('_filtermotart_cleaned_bp', '')]
    regex_subs = [
        ('_ts_masker.*/sar', '/smooth/'),
        ('_ts_masker.*/ar', '/unsmooth/'),
        ('_combiner.*/sar', '/smooth/'),
        ('_combiner.*/ar', '/unsmooth/'),
        ('_aparc_ts.*/sar', '/smooth/'),
        ('_aparc_ts.*/ar', '/unsmooth/'),
        ('_getsubcortts.*/sar', '/smooth/'),
        ('_getsubcortts.*/ar', '/unsmooth/'),
        ('series/sar', 'series/smooth/'),
        ('series/ar', 'series/unsmooth/'),
        ('_inverse_transform./', ''),
    ]
    # Save the relevant data into an output directory
    datasink = Node(interface=DataSink(), name="datasink")
    datasink.inputs.base_directory = sink_directory
    datasink.inputs.container = subject_id
    datasink.inputs.substitutions = substitutions
    datasink.inputs.regexp_substitutions = regex_subs  # (r'(/_.*(\d+/))', r'/run\2')
    wf.connect(realign, 'realignment_parameters', datasink,
               'resting.qa.motion')
    wf.connect(art, 'norm_files', datasink, 'resting.qa.art.@norm')
    wf.connect(art, 'intensity_files', datasink, 'resting.qa.art.@intensity')
    wf.connect(art, 'outlier_files', datasink, 'resting.qa.art.@outlier_files')
    wf.connect(registration, 'outputspec.segmentation_files', datasink,
               'resting.mask_files')
    wf.connect(registration, 'outputspec.anat2target', datasink,
               'resting.qa.ants')
    wf.connect(mask, 'mask_file', datasink, 'resting.mask_files.@brainmask')
    wf.connect(mask_target, 'out_file', datasink, 'resting.mask_files.target')
    wf.connect(filter1, 'out_f', datasink, 'resting.qa.compmaps.@mc_F')
    wf.connect(filter1, 'out_pf', datasink, 'resting.qa.compmaps.@mc_pF')
    wf.connect(filter2, 'out_f', datasink, 'resting.qa.compmaps')
    wf.connect(filter2, 'out_pf', datasink, 'resting.qa.compmaps.@p')
    wf.connect(bandpass, 'out_files', datasink,
               'resting.timeseries.@bandpassed')
    wf.connect(smooth, 'smoothed_files', datasink,
               'resting.timeseries.@smoothed')
    wf.connect(createfilter1, 'out_files', datasink,
               'resting.regress.@regressors')
    wf.connect(createfilter2, 'out_files', datasink,
               'resting.regress.@compcorr')
    wf.connect(maskts, 'out_file', datasink, 'resting.timeseries.target')
    wf.connect(sampleaparc, 'summary_file', datasink,
               'resting.parcellations.aparc')
    wf.connect(sampleaparc, 'avgwf_txt_file', datasink,
               'resting.parcellations.aparc.@avgwf')
    wf.connect(ts2txt, 'out_file', datasink,
               'resting.parcellations.grayo.@subcortical')

    datasink2 = Node(interface=DataSink(), name="datasink2")
    datasink2.inputs.base_directory = sink_directory
    datasink2.inputs.container = subject_id
    datasink2.inputs.substitutions = substitutions
    datasink2.inputs.regexp_substitutions = regex_subs  # (r'(/_.*(\d+/))', r'/run\2')
    wf.connect(combiner, 'out_file', datasink2,
               'resting.parcellations.grayo.@surface')
    return wf


"""
Creates the full workflow including getting information from dicom files
"""


def create_resting_workflow(args, name=None):
    TR = args.TR
    slice_times = args.slice_times
    if args.dicom_file:
        TR, slice_times, slice_thickness = get_info(args.dicom_file)
        slice_times = (np.array(slice_times) / 1000.).tolist()
    if name is None:
        name = 'resting_' + args.subject_id
    kwargs = dict(
        files=[os.path.abspath(filename) for filename in args.files],
        target_file=os.path.abspath(args.target_file),
        subject_id=args.subject_id,
        TR=TR,
        slice_times=slice_times,
        vol_fwhm=args.vol_fwhm,
        surf_fwhm=args.surf_fwhm,
        norm_threshold=2.,
        subjects_dir=os.path.abspath(args.fsdir),
        target_subject=args.target_surfs,
        lowpass_freq=args.lowpass_freq,
        highpass_freq=args.highpass_freq,
        sink_directory=os.path.abspath(args.sink),
        name=name)
    wf = create_workflow(**kwargs)
    return wf


if __name__ == "__main__":
    from argparse import ArgumentParser, RawTextHelpFormatter
    defstr = ' (default %(default)s)'
    parser = ArgumentParser(
        description=__doc__, formatter_class=RawTextHelpFormatter)
    parser.add_argument(
        "-d",
        "--dicom_file",
        dest="dicom_file",
        help="an example dicom file from the resting series")
    parser.add_argument(
        "-f",
        "--files",
        dest="files",
        nargs="+",
        help="4d nifti files for resting state",
        required=True)
    parser.add_argument(
        "-t",
        "--target",
        dest="target_file",
        help=("Target in MNI space. Best to use the MindBoggle "
              "template - "
              "OASIS-30_Atropos_template_in_MNI152_2mm.nii.gz"),
        required=True)
    parser.add_argument(
        "-s",
        "--subject_id",
        dest="subject_id",
        help="FreeSurfer subject id",
        required=True)
    parser.add_argument(
        "--subjects_dir",
        dest="fsdir",
        help="FreeSurfer subject directory",
        required=True)
    parser.add_argument(
        "--target_surfaces",
        dest="target_surfs",
        nargs="+",
        default=['fsaverage5'],
        help="FreeSurfer target surfaces" + defstr)
    parser.add_argument(
        "--TR",
        dest="TR",
        default=None,
        type=float,
        help="TR if dicom not provided in seconds")
    parser.add_argument(
        "--slice_times",
        dest="slice_times",
        nargs="+",
        type=float,
        help="Slice onset times in seconds")
    parser.add_argument(
        '--vol_fwhm',
        default=6.,
        dest='vol_fwhm',
        type=float,
        help="Spatial FWHM" + defstr)
    parser.add_argument(
        '--surf_fwhm',
        default=15.,
        dest='surf_fwhm',
        type=float,
        help="Spatial FWHM" + defstr)
    parser.add_argument(
        "-l",
        "--lowpass_freq",
        dest="lowpass_freq",
        default=0.1,
        type=float,
        help="Low pass frequency (Hz)" + defstr)
    parser.add_argument(
        "-u",
        "--highpass_freq",
        dest="highpass_freq",
        default=0.01,
        type=float,
        help="High pass frequency (Hz)" + defstr)
    parser.add_argument(
        "-o",
        "--output_dir",
        dest="sink",
        help="Output directory base",
        required=True)
    parser.add_argument(
        "-w", "--work_dir", dest="work_dir", help="Output directory base")
    parser.add_argument(
        "-p",
        "--plugin",
        dest="plugin",
        default='Linear',
        help="Plugin to use")
    parser.add_argument(
        "--plugin_args", dest="plugin_args", help="Plugin arguments")
    args = parser.parse_args()

    wf = create_resting_workflow(args)

    if args.work_dir:
        work_dir = os.path.abspath(args.work_dir)
    else:
        work_dir = os.getcwd()

    wf.base_dir = work_dir
    if args.plugin_args:
        wf.run(args.plugin, plugin_args=eval(args.plugin_args))
    else:
        wf.run(args.plugin)