#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
#
# @Author: oesteban
# @Date: 2016-01-05 16:15:08
# @Email: code@oscaresteban.es
"""
=======================
The functional workflow
=======================
.. image :: _static/functional_workflow_source.svg
The functional workflow follows the following steps:
#. Conform (reorientations, revise data types) input data, read
associated metadata and discard non-steady state frames
(:py:func:`mriqc.utils.misc.reorient_and_discard_non_steady`).
#. :abbr:`HMC (head-motion correction)` based on ``3dvolreg`` from
AFNI -- :py:func:`hmc_afni`.
#. Skull-stripping of the time-series (AFNI) --
:py:func:`fmri_bmsk_workflow`.
#. Calculate mean time-series, and :abbr:`tSNR (temporal SNR)`.
#. Spatial Normalization to MNI (ANTs) -- :py:func:`epi_mni_align`
#. Extraction of IQMs -- :py:func:`compute_iqms`.
#. Individual-reports generation -- :py:func:`individual_reports`.
This workflow is orchestrated by :py:func:`fmri_qc_workflow`.
"""
from __future__ import print_function, division, absolute_import, unicode_literals
import os.path as op
from niworkflows.nipype.pipeline import engine as pe
from niworkflows.nipype.algorithms import confounds as nac
from niworkflows.nipype.interfaces import io as nio
from niworkflows.nipype.interfaces import utility as niu
from niworkflows.nipype.interfaces import afni, ants, fsl
from .. import DEFAULTS, logging
from ..interfaces import ReadSidecarJSON, FunctionalQC, Spikes, IQMFileSink
from ..utils.misc import check_folder, reorient_and_discard_non_steady
from niworkflows.interfaces import segmentation as nws
from niworkflows.interfaces import registration as nwr
DEFAULT_FD_RADIUS = 50.
WFLOGGER = logging.getLogger('mriqc.workflow')
[docs]def fmri_qc_workflow(dataset, settings, name='funcMRIQC'):
"""
The fMRI qc workflow
.. workflow::
import os.path as op
from mriqc.workflows.functional import fmri_qc_workflow
datadir = op.abspath('data')
wf = fmri_qc_workflow([op.join(datadir, 'sub-001/func/sub-001_task-rest_bold.nii.gz')],
settings={'bids_dir': datadir,
'output_dir': op.abspath('out'),
'no_sub': True})
"""
workflow = pe.Workflow(name=name)
biggest_file_gb = settings.get("biggest_file_size_gb", 1)
# Define workflow, inputs and outputs
# 0. Get data, put it in RAS orientation
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']), name='inputnode')
WFLOGGER.info('Building fMRI QC workflow, datasets list: %s',
sorted([d.replace(settings['bids_dir'] + '/', '') for d in dataset]))
inputnode.iterables = [('in_file', dataset)]
outputnode = pe.Node(niu.IdentityInterface(
fields=['qc', 'mosaic', 'out_group', 'out_dvars',
'out_fd']), name='outputnode')
reorient_and_discard = pe.Node(niu.Function(input_names=['in_file', 'float32'],
output_names=['exclude_index',
'out_file'],
function=reorient_and_discard_non_steady),
name='reorient_and_discard')
reorient_and_discard.inputs.float32 = settings.get("float32", DEFAULTS['float32'])
reorient_and_discard.interface.estimated_memory_gb = 4.0 * biggest_file_gb
# Workflow --------------------------------------------------------
# 1. HMC: head motion correct
if settings.get('hmc_fsl', False):
hmcwf = hmc_mcflirt(settings)
else:
hmcwf = hmc_afni(settings,
st_correct=settings.get('correct_slice_timing', False),
despike=settings.get('despike', False),
deoblique=settings.get('deoblique', False),
start_idx=settings.get('start_idx', None),
stop_idx=settings.get('stop_idx', None))
# Set HMC settings
hmcwf.inputs.inputnode.fd_radius = settings.get('fd_radius', DEFAULT_FD_RADIUS)
mean = pe.Node(afni.TStat( # 2. Compute mean fmri
options='-mean', outputtype='NIFTI_GZ'), name='mean')
mean.interface.estimated_memory_gb = biggest_file_gb * 1.5
skullstrip_epi = fmri_bmsk_workflow(use_bet=True)
# EPI to MNI registration
ema = epi_mni_align(settings)
# Compute TSNR using nipype implementation
tsnr = pe.Node(nac.TSNR(), name='compute_tsnr')
tsnr.interface.estimated_memory_gb = biggest_file_gb * 4.5
# 7. Compute IQMs
iqmswf = compute_iqms(settings)
# Reports
repwf = individual_reports(settings)
workflow.connect([
(inputnode, iqmswf, [('in_file', 'inputnode.in_file')]),
(inputnode, reorient_and_discard, [('in_file', 'in_file')]),
(reorient_and_discard, hmcwf, [('out_file', 'inputnode.in_file')]),
(mean, skullstrip_epi, [('out_file', 'inputnode.in_file')]),
(hmcwf, mean, [('outputnode.out_file', 'in_file')]),
(hmcwf, tsnr, [('outputnode.out_file', 'in_file')]),
(mean, ema, [('out_file', 'inputnode.epi_mean')]),
(skullstrip_epi, ema, [('outputnode.out_file', 'inputnode.epi_mask')]),
(reorient_and_discard, iqmswf, [('out_file', 'inputnode.in_ras')]),
(mean, iqmswf, [('out_file', 'inputnode.epi_mean')]),
(hmcwf, iqmswf, [('outputnode.out_file', 'inputnode.hmc_epi'),
('outputnode.out_fd', 'inputnode.hmc_fd')]),
(skullstrip_epi, iqmswf, [('outputnode.out_file', 'inputnode.brainmask')]),
(tsnr, iqmswf, [('tsnr_file', 'inputnode.in_tsnr')]),
(reorient_and_discard, repwf, [('out_file', 'inputnode.in_ras')]),
(mean, repwf, [('out_file', 'inputnode.epi_mean')]),
(tsnr, repwf, [('stddev_file', 'inputnode.in_stddev')]),
(skullstrip_epi, repwf, [('outputnode.out_file', 'inputnode.brainmask')]),
(hmcwf, repwf, [('outputnode.out_fd', 'inputnode.hmc_fd'),
('outputnode.out_file', 'inputnode.hmc_epi')]),
(ema, repwf, [('outputnode.epi_parc', 'inputnode.epi_parc'),
('outputnode.report', 'inputnode.mni_report')]),
(reorient_and_discard, iqmswf, [('exclude_index', 'inputnode.exclude_index')]),
(iqmswf, repwf, [('outputnode.out_file', 'inputnode.in_iqms'),
('outputnode.out_dvars', 'inputnode.in_dvars'),
('outputnode.outliers', 'inputnode.outliers')]),
(hmcwf, outputnode, [('outputnode.out_fd', 'out_fd')]),
])
if settings.get('fft_spikes_detector', False):
workflow.connect([
(iqmswf, repwf, [('outputnode.out_spikes', 'inputnode.in_spikes'),
('outputnode.out_fft', 'inputnode.in_fft')]),
])
if settings.get('ica', False):
melodic = pe.Node(nws.MELODICRPT(no_bet=True,
no_mask=True,
no_mm=True,
generate_report=True), name="ICA")
melodic.interface.estimated_memory_gb = biggest_file_gb * 5
workflow.connect([
(reorient_and_discard, melodic, [('out_file', 'in_files')]),
(skullstrip_epi, melodic, [('outputnode.out_file', 'report_mask')]),
(melodic, repwf, [('out_report', 'inputnode.ica_report')])
])
# Upload metrics
if not settings.get('no_sub', False):
from ..interfaces.webapi import UploadIQMs
upldwf = pe.Node(UploadIQMs(), name='UploadMetrics')
upldwf.inputs.url = settings.get('webapi_url')
if settings.get('webapi_port'):
upldwf.inputs.port = settings.get('webapi_port')
upldwf.inputs.email = settings.get('email')
upldwf.inputs.strict = settings.get('upload_strict', False)
workflow.connect([
(iqmswf, upldwf, [('outputnode.out_file', 'in_iqms')]),
])
return workflow
[docs]def compute_iqms(settings, name='ComputeIQMs'):
"""
Workflow that actually computes the IQMs
.. workflow::
from mriqc.workflows.functional import compute_iqms
wf = compute_iqms(settings={'output_dir': 'out'})
"""
from .utils import _tofloat
from ..interfaces.transitional import GCOR
biggest_file_gb = settings.get("biggest_file_size_gb", 1)
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=[
'in_file', 'in_ras',
'epi_mean', 'brainmask', 'hmc_epi', 'hmc_fd', 'fd_thres', 'in_tsnr', 'metadata',
'exclude_index']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_dvars', 'outliers', 'out_spikes', 'out_fft']),
name='outputnode')
# Set FD threshold
inputnode.inputs.fd_thres = settings.get('fd_thres', 0.2)
deriv_dir = check_folder(op.abspath(op.join(settings['output_dir'], 'derivatives')))
# Compute DVARS
dvnode = pe.Node(nac.ComputeDVARS(save_plot=False, save_all=True), name='ComputeDVARS')
dvnode.interface.estimated_memory_gb = biggest_file_gb * 3
# AFNI quality measures
fwhm = pe.Node(afni.FWHMx(combine=True, detrend=True), name='smoothness')
# fwhm.inputs.acf = True # add when AFNI >= 16
outliers = pe.Node(afni.OutlierCount(fraction=True, out_file='ouliers.out'),
name='outliers')
outliers.interface.estimated_memory_gb = biggest_file_gb * 2.5
quality = pe.Node(afni.QualityIndex(automask=True), out_file='quality.out',
name='quality')
quality.interface.estimated_memory_gb = biggest_file_gb * 3
gcor = pe.Node(GCOR(), name='gcor', estimated_memory_gb=biggest_file_gb * 2)
measures = pe.Node(FunctionalQC(), name='measures')
measures.interface.estimated_memory_gb = biggest_file_gb * 3
workflow.connect([
(inputnode, dvnode, [('hmc_epi', 'in_file'),
('brainmask', 'in_mask')]),
(inputnode, measures, [('epi_mean', 'in_epi'),
('brainmask', 'in_mask'),
('hmc_epi', 'in_hmc'),
('hmc_fd', 'in_fd'),
('fd_thres', 'fd_thres'),
('in_tsnr', 'in_tsnr')]),
(inputnode, fwhm, [('epi_mean', 'in_file'),
('brainmask', 'mask')]),
(inputnode, quality, [('hmc_epi', 'in_file')]),
(inputnode, outliers, [('hmc_epi', 'in_file'),
('brainmask', 'mask')]),
(inputnode, gcor, [('hmc_epi', 'in_file'),
('brainmask', 'mask')]),
(dvnode, measures, [('out_all', 'in_dvars')]),
(fwhm, measures, [(('fwhm', _tofloat), 'in_fwhm')]),
(dvnode, outputnode, [('out_all', 'out_dvars')]),
(outliers, outputnode, [('out_file', 'outliers')])
])
# Add metadata
meta = pe.Node(ReadSidecarJSON(), name='metadata')
addprov = pe.Node(niu.Function(function=_add_provenance), name='provenance')
addprov.inputs.settings = {
'fd_thres': settings.get('fd_thres', 0.2),
'hmc_fsl': settings.get('hmc_fsl', True),
}
# Save to JSON file
datasink = pe.Node(IQMFileSink(
modality='bold', out_dir=deriv_dir), name='datasink')
workflow.connect([
(inputnode, datasink, [('exclude_index', 'dummy_trs')]),
(inputnode, meta, [('in_file', 'in_file')]),
(inputnode, addprov, [('in_file', 'in_file')]),
(meta, datasink, [('subject_id', 'subject_id'),
('session_id', 'session_id'),
('task_id', 'task_id'),
('acq_id', 'acq_id'),
('rec_id', 'rec_id'),
('run_id', 'run_id'),
('out_dict', 'metadata')]),
(addprov, datasink, [('out', 'provenance')]),
(outliers, datasink, [(('out_file', _parse_tout), 'aor')]),
(gcor, datasink, [(('out', _tofloat), 'gcor')]),
(quality, datasink, [(('out_file', _parse_tqual), 'aqi')]),
(measures, datasink, [('out_qc', 'root')]),
(datasink, outputnode, [('out_file', 'out_file')])
])
# FFT spikes finder
if settings.get('fft_spikes_detector', False):
from .utils import slice_wise_fft
spikes_fft = pe.Node(niu.Function(
input_names=['in_file'],
output_names=['n_spikes', 'out_spikes', 'out_fft'],
function=slice_wise_fft), name='SpikesFinderFFT')
workflow.connect([
(inputnode, spikes_fft, [('in_ras', 'in_file')]),
(spikes_fft, outputnode, [('out_spikes', 'out_spikes'),
('out_fft', 'out_fft')]),
(spikes_fft, datasink, [('n_spikes', 'spikes_num')])
])
return workflow
[docs]def individual_reports(settings, name='ReportsWorkflow'):
"""
Encapsulates nodes writing plots
.. workflow::
from mriqc.workflows.functional import individual_reports
wf = individual_reports(settings={'output_dir': 'out'})
"""
from ..interfaces import PlotMosaic, PlotSpikes
from ..reports import individual_html
verbose = settings.get('verbose_reports', False)
biggest_file_gb = settings.get("biggest_file_size_gb", 1)
pages = 5
extra_pages = 0
if verbose:
extra_pages = 4
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=[
'in_iqms', 'in_ras', 'hmc_epi', 'epi_mean', 'brainmask', 'hmc_fd', 'fd_thres', 'epi_parc',
'in_dvars', 'in_stddev', 'outliers', 'in_spikes', 'in_fft',
'mni_report', 'ica_report']),
name='inputnode')
# Set FD threshold
inputnode.inputs.fd_thres = settings.get('fd_thres', 0.2)
spmask = pe.Node(niu.Function(
input_names=['in_file', 'in_mask'], output_names=['out_file', 'out_plot'],
function=spikes_mask), name='SpikesMask')
spmask.interface.estimated_memory_gb = biggest_file_gb * 3.5
spikes_bg = pe.Node(Spikes(no_zscore=True, detrend=False), name='SpikesFinderBgMask')
spikes_bg.interface.estimated_memory_gb = biggest_file_gb * 2.5
bigplot = pe.Node(niu.Function(
input_names=['in_func', 'in_mask', 'in_segm', 'in_spikes_bg',
'fd', 'fd_thres', 'dvars', 'outliers'],
output_names=['out_file'], function=_big_plot), name='BigPlot')
bigplot.interface.estimated_memory_gb = biggest_file_gb * 3.5
workflow.connect([
(inputnode, spikes_bg, [('in_ras', 'in_file')]),
(inputnode, spmask, [('in_ras', 'in_file')]),
(inputnode, bigplot, [('hmc_epi', 'in_func'),
('brainmask', 'in_mask'),
('hmc_fd', 'fd'),
('fd_thres', 'fd_thres'),
('in_dvars', 'dvars'),
('epi_parc', 'in_segm'),
('outliers', 'outliers')]),
(spikes_bg, bigplot, [('out_tsz', 'in_spikes_bg')]),
(spmask, spikes_bg, [('out_file', 'in_mask')]),
])
mosaic_mean = pe.Node(PlotMosaic(
out_file='plot_func_mean_mosaic1.svg',
title='EPI mean session',
cmap='Greys_r'),
name='PlotMosaicMean')
mosaic_stddev = pe.Node(PlotMosaic(
out_file='plot_func_stddev_mosaic2_stddev.svg',
title='EPI SD session',
cmap='viridis'), name='PlotMosaicSD')
mplots = pe.Node(niu.Merge(pages + extra_pages
+ int(settings.get('fft_spikes_detector', False))
+ int(settings.get('ica', False))),
name='MergePlots')
rnode = pe.Node(niu.Function(
input_names=['in_iqms', 'in_plots'], output_names=['out_file'],
function=individual_html), name='GenerateReport')
# Link images that should be reported
dsplots = pe.Node(nio.DataSink(
base_directory=settings['output_dir'], parameterization=False), name='dsplots')
dsplots.inputs.container = 'reports'
workflow.connect([
(inputnode, rnode, [('in_iqms', 'in_iqms')]),
(inputnode, mosaic_mean, [('epi_mean', 'in_file')]),
(inputnode, mosaic_stddev, [('in_stddev', 'in_file')]),
(mosaic_mean, mplots, [('out_file', 'in1')]),
(mosaic_stddev, mplots, [('out_file', 'in2')]),
(bigplot, mplots, [('out_file', 'in3')]),
(mplots, rnode, [('out', 'in_plots')]),
(rnode, dsplots, [('out_file', '@html_report')]),
])
if settings.get('fft_spikes_detector', False):
mosaic_spikes = pe.Node(PlotSpikes(
out_file='plot_spikes.svg', cmap='viridis',
title='High-Frequency spikes'),
name='PlotSpikes')
workflow.connect([
(inputnode, mosaic_spikes, [('in_ras', 'in_file'),
('in_spikes', 'in_spikes'),
('in_fft', 'in_fft')]),
(mosaic_spikes, mplots, [('out_file', 'in4')])
])
if settings.get('ica', False):
page_number = 4
if settings.get('fft_spikes_detector', False):
page_number += 1
workflow.connect([
(inputnode, mplots, [('ica_report', 'in%d'%page_number)])
])
if not verbose:
return workflow
mosaic_zoom = pe.Node(PlotMosaic(
out_file='plot_anat_mosaic1_zoomed.svg',
title='Zoomed-in EPI mean',
cmap='Greys_r'), name='PlotMosaicZoomed')
mosaic_noise = pe.Node(PlotMosaic(
out_file='plot_anat_mosaic2_noise.svg',
title='Enhanced noise in EPI mean',
only_noise=True, cmap='viridis_r'), name='PlotMosaicNoise')
# Verbose-reporting goes here
from ..interfaces.viz import PlotContours
from ..viz.utils import plot_bg_dist
plot_bmask = pe.Node(PlotContours(
display_mode='z', levels=[.5], colors=['r'], cut_coords=10,
out_file='bmask'), name='PlotBrainmask')
workflow.connect([
(inputnode, plot_bmask, [('epi_mean', 'in_file'),
('brainmask', 'in_contours')]),
(inputnode, mosaic_zoom, [('epi_mean', 'in_file'),
('brainmask', 'bbox_mask_file')]),
(inputnode, mosaic_noise, [('epi_mean', 'in_file')]),
(mosaic_zoom, mplots, [('out_file', 'in%d' % (pages + 1))]),
(mosaic_noise, mplots, [('out_file', 'in%d' % (pages + 2))]),
(plot_bmask, mplots, [('out_file', 'in%d' % (pages + 3))]),
(inputnode, mplots, [('mni_report', 'in%d' % (pages + 4))]),
])
return workflow
[docs]def fmri_bmsk_workflow(name='fMRIBrainMask', use_bet=False):
"""
Computes a brain mask for the input :abbr:`fMRI (functional MRI)`
dataset
.. workflow::
from mriqc.workflows.functional import fmri_bmsk_workflow
wf = fmri_bmsk_workflow()
"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['in_file']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['out_file']),
name='outputnode')
if not use_bet:
afni_msk = pe.Node(afni.Automask(
outputtype='NIFTI_GZ'), name='afni_msk')
# Connect brain mask extraction
workflow.connect([
(inputnode, afni_msk, [('in_file', 'in_file')]),
(afni_msk, outputnode, [('out_file', 'out_file')])
])
else:
bet_msk = pe.Node(fsl.BET(mask=True, functional=True), name='bet_msk')
erode = pe.Node(fsl.ErodeImage(), name='erode')
# Connect brain mask extraction
workflow.connect([
(inputnode, bet_msk, [('in_file', 'in_file')]),
(bet_msk, erode, [('mask_file', 'in_file')]),
(erode, outputnode, [('out_file', 'out_file')])
])
return workflow
[docs]def hmc_mcflirt(settings, name='fMRI_HMC_mcflirt'):
"""
An :abbr:`HMC (head motion correction)` for functional scans
using FSL MCFLIRT
.. workflow::
from mriqc.workflows.functional import hmc_mcflirt
wf = hmc_mcflirt({'biggest_file_size_gb': 1})
"""
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'fd_radius', 'start_idx', 'stop_idx']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_fd']), name='outputnode')
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"), name="gen_ref")
mcflirt = pe.Node(fsl.MCFLIRT(save_plots=True, interpolation='sinc'),
name='MCFLIRT')
mcflirt.interface.estimated_memory_gb = settings[
"biggest_file_size_gb"] * 2.5
fdnode = pe.Node(nac.FramewiseDisplacement(normalize=False,
parameter_source="FSL"),
name='ComputeFD')
workflow.connect([
(inputnode, gen_ref, [('in_file', 'in_file')]),
(gen_ref, mcflirt, [('ref_image', 'ref_file')]),
(inputnode, mcflirt, [('in_file', 'in_file')]),
(inputnode, fdnode, [('fd_radius', 'radius')]),
(mcflirt, fdnode, [('par_file', 'in_file')]),
(mcflirt, outputnode, [('out_file', 'out_file')]),
(fdnode, outputnode, [('out_file', 'out_fd')]),
])
return workflow
[docs]def hmc_afni(settings, name='fMRI_HMC_afni', st_correct=False, despike=False,
deoblique=False, start_idx=None, stop_idx=None):
"""
A :abbr:`HMC (head motion correction)` workflow for
functional scans
.. workflow::
from mriqc.workflows.functional import hmc_afni
wf = hmc_afni({'biggest_file_size_gb': 1})
"""
biggest_file_gb = settings.get("biggest_file_size_gb", 1)
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['in_file', 'fd_radius', 'start_idx', 'stop_idx']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['out_file', 'out_fd']), name='outputnode')
if (start_idx is not None) or (stop_idx is not None):
drop_trs = pe.Node(afni.Calc(expr='a', outputtype='NIFTI_GZ'),
name='drop_trs')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'in_file_a'),
('start_idx', 'start_idx'),
('stop_idx', 'stop_idx')]),
])
else:
drop_trs = pe.Node(niu.IdentityInterface(fields=['out_file']),
name='drop_trs')
workflow.connect([
(inputnode, drop_trs, [('in_file', 'out_file')]),
])
gen_ref = pe.Node(nwr.EstimateReferenceImage(mc_method="AFNI"), name="gen_ref")
# calculate hmc parameters
hmc = pe.Node(
afni.Volreg(args='-Fourier -twopass', zpad=4, outputtype='NIFTI_GZ'),
name='motion_correct')
hmc.interface.estimated_memory_gb = biggest_file_gb * 2.5
# Compute the frame-wise displacement
fdnode = pe.Node(nac.FramewiseDisplacement(normalize=False,
parameter_source="AFNI"),
name='ComputeFD')
workflow.connect([
(inputnode, fdnode, [('fd_radius', 'radius')]),
(gen_ref, hmc, [('ref_image', 'basefile')]),
(hmc, outputnode, [('out_file', 'out_file')]),
(hmc, fdnode, [('oned_file', 'in_file')]),
(fdnode, outputnode, [('out_file', 'out_fd')]),
])
# Slice timing correction, despiking, and deoblique
st_corr = pe.Node(afni.TShift(outputtype='NIFTI_GZ'), name='TimeShifts')
deoblique_node = pe.Node(afni.Refit(deoblique=True), name='deoblique')
despike_node = pe.Node(afni.Despike(outputtype='NIFTI_GZ'), name='despike')
if st_correct and despike and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct and despike:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, despike_node, [('out_file', 'in_file')]),
(despike_node, gen_ref, [('out_file', 'in_file')]),
(despike_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct and deoblique:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif st_correct:
workflow.connect([
(drop_trs, st_corr, [('out_file', 'in_file')]),
(st_corr, gen_ref, [('out_file', 'in_file')]),
(st_corr, hmc, [('out_file', 'in_file')]),
])
elif despike and deoblique:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
elif despike:
workflow.connect([
(drop_trs, despike_node, [('out_file', 'in_file')]),
(despike_node, gen_ref, [('out_file', 'in_file')]),
(despike_node, hmc, [('out_file', 'in_file')]),
])
elif deoblique:
workflow.connect([
(drop_trs, deoblique_node, [('out_file', 'in_file')]),
(deoblique_node, gen_ref, [('out_file', 'in_file')]),
(deoblique_node, hmc, [('out_file', 'in_file')]),
])
else:
workflow.connect([
(drop_trs, gen_ref, [('out_file', 'in_file')]),
(drop_trs, hmc, [('out_file', 'in_file')]),
])
return workflow
[docs]def epi_mni_align(settings, name='SpatialNormalization'):
"""
Uses FSL FLIRT with the BBR cost function to find the transform that
maps the EPI space into the MNI152-nonlinear-symmetric atlas.
The input epi_mean is the averaged and brain-masked EPI timeseries
Returns the EPI mean resampled in MNI space (for checking out registration) and
the associated "lobe" parcellation in EPI space.
.. workflow::
from mriqc.workflows.functional import epi_mni_align
wf = epi_mni_align({})
"""
from niworkflows.data import get_mni_icbm152_nlin_asym_09c as get_template
from niworkflows.interfaces.registration import RobustMNINormalizationRPT as RobustMNINormalization
from pkg_resources import resource_filename as pkgrf
# Get settings
testing = settings.get('testing', False)
n_procs = settings.get('n_procs', 1)
ants_nthreads = settings.get('ants_nthreads', DEFAULTS['ants_nthreads'])
# Init template
mni_template = get_template()
workflow = pe.Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(fields=['epi_mean', 'epi_mask']),
name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(
fields=['epi_mni', 'epi_parc', 'report']), name='outputnode')
epimask = pe.Node(fsl.ApplyMask(), name='EPIApplyMask')
n4itk = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='SharpenEPI')
norm = pe.Node(RobustMNINormalization(
num_threads=ants_nthreads,
template='mni_icbm152_nlin_asym_09c',
reference_image=pkgrf('mriqc', 'data/mni/2mm_T2_brain.nii.gz'),
flavor='testing' if testing else 'precise',
moving='EPI',
generate_report=True,),
name='EPI2MNI',
num_threads=n_procs,
estimated_memory_gb=3)
# Warp segmentation into EPI space
invt = pe.Node(ants.ApplyTransforms(float=True,
input_image=op.join(mni_template, '1mm_parc.nii.gz'),
dimension=3, default_value=0, interpolation='NearestNeighbor'),
name='ResampleSegmentation')
workflow.connect([
(inputnode, invt, [('epi_mean', 'reference_image')]),
(inputnode, n4itk, [('epi_mean', 'input_image')]),
(inputnode, epimask, [('epi_mask', 'mask_file')]),
(n4itk, epimask, [('output_image', 'in_file')]),
(epimask, norm, [('out_file', 'moving_image')]),
(norm, invt, [
('inverse_composite_transform', 'transforms')]),
(invt, outputnode, [('output_image', 'epi_parc')]),
(norm, outputnode, [('warped_image', 'epi_mni'),
('out_report', 'report')]),
])
return workflow
[docs]def spikes_mask(in_file, in_mask=None, out_file=None):
"""
Utility function to calculate a mask in which check
for :abbr:`EM (electromagnetic)` spikes.
"""
import os.path as op
import nibabel as nb
import numpy as np
from nilearn.image import mean_img
from nilearn.plotting import plot_roi
from scipy import ndimage as nd
if out_file is None:
fname, ext = op.splitext(op.basename(in_file))
if ext == '.gz':
fname, ext2 = op.splitext(fname)
ext = ext2 + ext
out_file = op.abspath('{}_spmask{}'.format(fname, ext))
out_plot = op.abspath('{}_spmask.pdf'.format(fname))
in_4d_nii = nb.load(in_file)
orientation = nb.aff2axcodes(in_4d_nii.affine)
if in_mask:
mask_data = nb.load(in_mask).get_data()
a = np.where(mask_data != 0)
bbox = np.max(a[0]) - np.min(a[0]), np.max(a[1]) - \
np.min(a[1]), np.max(a[2]) - np.min(a[2])
longest_axis = np.argmax(bbox)
# Input here is a binarized and intersected mask data from previous section
dil_mask = nd.binary_dilation(
mask_data, iterations=int(mask_data.shape[longest_axis]/9))
rep = list(mask_data.shape)
rep[longest_axis] = -1
new_mask_2d = dil_mask.max(axis=longest_axis).reshape(rep)
rep = [1, 1, 1]
rep[longest_axis] = mask_data.shape[longest_axis]
new_mask_3d = np.logical_not(np.tile(new_mask_2d, rep))
else:
new_mask_3d = np.zeros(in_4d_nii.shape[:3]) == 1
if orientation[0] in ['L', 'R']:
new_mask_3d[0:2, :, :] = True
new_mask_3d[-3:-1, :, :] = True
else:
new_mask_3d[:, 0:2, :] = True
new_mask_3d[:, -3:-1, :] = True
mask_nii = nb.Nifti1Image(new_mask_3d.astype(np.uint8), in_4d_nii.get_affine(),
in_4d_nii.get_header())
mask_nii.to_filename(out_file)
plot_roi(mask_nii, mean_img(in_4d_nii), output_file=out_plot)
return out_file, out_plot
def _add_provenance(in_file, settings):
from mriqc import __version__ as version
from niworkflows.nipype.utils.filemanip import hash_infile
out_prov = {
'md5sum': hash_infile(in_file),
'version': version,
'software': 'mriqc'
}
if settings:
out_prov['settings'] = settings
return out_prov
def _mean(inlist):
import numpy as np
return np.mean(inlist)
def _parse_tqual(in_file):
import numpy as np
with open(in_file, 'r') as fin:
lines = fin.readlines()
# remove general information
lines = [l for l in lines if l[:2] != '++']
# remove general information and warnings
return np.mean([float(l.strip()) for l in lines])
raise RuntimeError('AFNI 3dTqual was not parsed correctly')
def _parse_tout(in_file):
import numpy as np
data = np.loadtxt(in_file) # pylint: disable=no-member
return data.mean()
def _big_plot(in_func, in_mask, in_segm, in_spikes_bg,
fd, fd_thres, dvars, outliers, out_file=None):
import os.path as op
import numpy as np
from mriqc.viz.fmriplots import fMRIPlot
if out_file is None:
fname, ext = op.splitext(op.basename(in_func))
if ext == '.gz':
fname, _ = op.splitext(fname)
out_file = op.abspath('{}_fmriplot.svg'.format(fname))
title = 'fMRI Summary plot'
myplot = fMRIPlot(
in_func, in_mask, in_segm, title=title)
myplot.add_spikes(np.loadtxt(in_spikes_bg), zscored=False)
# Add AFNI ouliers plot
myplot.add_confounds([np.nan] + np.loadtxt(outliers, usecols=[0]).tolist(),
{'name': 'ouliers', 'units': '%', 'normalize': False,
'ylims': (0.0, None)})
# Pick non-standardize dvars
myplot.add_confounds([np.nan] + np.loadtxt(dvars, skiprows=1,
usecols=[1]).tolist(),
{'name': 'DVARS', 'units': None, 'normalize': False})
# Add FD
myplot.add_confounds([np.nan] + np.loadtxt(fd, skiprows=1,
usecols=[0]).tolist(),
{'name': 'FD', 'units': 'mm', 'normalize': False,
'cutoff': [fd_thres], 'ylims': (0.0, fd_thres)})
myplot.plot()
myplot.fig.savefig(out_file, bbox_inches='tight')
myplot.fig.clf()
return out_file