#!/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:
"""
.. _sdc_direct_b0 :
Direct B0 mapping sequences
~~~~~~~~~~~~~~~~~~~~~~~~~~~
When the fieldmap is directly measured with a prescribed sequence (such as
:abbr:`SE (spiral echo)`), we only need to calculate the corresponding B-Spline
coefficients to adapt the fieldmap to the TOPUP tool.
This procedure is described with more detail `here <https://cni.stanford.edu/\
wiki/GE_Processing#Fieldmaps>`__.
This corresponds to the section 8.9.3 --fieldmap image (and one magnitude image)--
of the BIDS specification.
"""
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu, fsl, ants
from nipype.workflows.dmri.fsl.utils import demean_image, cleanup_edge_pipeline
from niworkflows.interfaces.masks import BETRPT
from ...engine import Workflow
from ...interfaces import (
IntraModalMerge, DerivativesDataSink,
FieldEnhance, FieldToRadS, FieldToHz
)
[docs]def init_fmap_wf(omp_nthreads, fmap_bspline, name='fmap_wf'):
"""
Fieldmap workflow - when we have a sequence that directly measures the fieldmap
we just need to mask it (using the corresponding magnitude image) to remove the
noise in the surrounding air region, and ensure that units are Hz.
.. workflow ::
:graph2use: orig
:simple_form: yes
from fmriprep.workflows.fieldmap.fmap import init_fmap_wf
wf = init_fmap_wf(omp_nthreads=6, fmap_bspline=False)
"""
workflow = Workflow(name=name)
inputnode = pe.Node(niu.IdentityInterface(
fields=['magnitude', 'fieldmap']), name='inputnode')
outputnode = pe.Node(niu.IdentityInterface(fields=['fmap', 'fmap_ref', 'fmap_mask']),
name='outputnode')
# Merge input magnitude images
magmrg = pe.Node(IntraModalMerge(), name='magmrg')
# Merge input fieldmap images
fmapmrg = pe.Node(IntraModalMerge(zero_based_avg=False, hmc=False),
name='fmapmrg')
# de-gradient the fields ("bias/illumination artifact")
n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True),
name='n4_correct', n_procs=omp_nthreads)
bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
name='bet')
ds_fmap_mask = pe.Node(DerivativesDataSink(suffix='fmap_mask'),
name='ds_report_fmap_mask', run_without_submitting=True)
workflow.connect([
(inputnode, magmrg, [('magnitude', 'in_files')]),
(inputnode, fmapmrg, [('fieldmap', 'in_files')]),
(magmrg, n4_correct, [('out_file', 'input_image')]),
(n4_correct, bet, [('output_image', 'in_file')]),
(bet, outputnode, [('mask_file', 'fmap_mask'),
('out_file', 'fmap_ref')]),
(inputnode, ds_fmap_mask, [('fieldmap', 'source_file')]),
(bet, ds_fmap_mask, [('out_report', 'in_file')]),
])
if fmap_bspline:
# despike_threshold=1.0, mask_erode=1),
fmapenh = pe.Node(FieldEnhance(unwrap=False, despike=False),
name='fmapenh', mem_gb=4, n_procs=omp_nthreads)
workflow.connect([
(bet, fmapenh, [('mask_file', 'in_mask'),
('out_file', 'in_magnitude')]),
(fmapmrg, fmapenh, [('out_file', 'in_file')]),
(fmapenh, outputnode, [('out_file', 'fmap')]),
])
else:
torads = pe.Node(FieldToRadS(), name='torads')
prelude = pe.Node(fsl.PRELUDE(), name='prelude')
tohz = pe.Node(FieldToHz(), name='tohz')
denoise = pe.Node(fsl.SpatialFilter(operation='median', kernel_shape='sphere',
kernel_size=3), name='denoise')
demean = pe.Node(niu.Function(function=demean_image), name='demean')
cleanup_wf = cleanup_edge_pipeline(name='cleanup_wf')
applymsk = pe.Node(fsl.ApplyMask(), name='applymsk')
workflow.connect([
(bet, prelude, [('mask_file', 'mask_file'),
('out_file', 'magnitude_file')]),
(fmapmrg, torads, [('out_file', 'in_file')]),
(torads, tohz, [('fmap_range', 'range_hz')]),
(torads, prelude, [('out_file', 'phase_file')]),
(prelude, tohz, [('unwrapped_phase_file', 'in_file')]),
(tohz, denoise, [('out_file', 'in_file')]),
(denoise, demean, [('out_file', 'in_file')]),
(demean, cleanup_wf, [('out', 'inputnode.in_file')]),
(bet, cleanup_wf, [('mask_file', 'inputnode.in_mask')]),
(cleanup_wf, applymsk, [('outputnode.out_file', 'in_file')]),
(bet, applymsk, [('mask_file', 'mask_file')]),
(applymsk, outputnode, [('out_file', 'fmap')]),
])
return workflow