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Repair 3dQwarp workflow
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@psadil
psadil committed Jul 7, 2024
1 parent 08e198f commit 19677a1
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133 changes: 100 additions & 33 deletions sdcflows/workflows/fit/pepolar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,9 +21,8 @@
# https://www.nipreps.org/community/licensing/
#
"""Datasets with multiple phase encoded directions."""
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu

from nipype.pipeline import engine as pe
from niworkflows.engine.workflows import LiterateWorkflow as Workflow

from ... import data
Expand All @@ -32,7 +31,7 @@
_PEPOLAR_DESC = """\
A *B<sub>0</sub>*-nonuniformity map (or *fieldmap*) was estimated based on two (or more)
echo-planar imaging (EPI) references """

_PEPOLAR_METHOD = "PEB/PEPOLAR (phase-encoding based / PE-POLARity)"

def init_topup_wf(
grid_reference=0,
Expand Down Expand Up @@ -88,13 +87,13 @@ def init_topup_wf(
"""
from nipype.interfaces.fsl.epi import TOPUP
from niworkflows.interfaces.nibabel import MergeSeries, ReorientImage
from niworkflows.interfaces.images import RobustAverage
from niworkflows.interfaces.nibabel import MergeSeries, ReorientImage

from ...utils.misc import front as _front
from ...interfaces.epi import GetReadoutTime, SortPEBlips
from ...interfaces.utils import UniformGrid, PadSlices, ReorientImageAndMetadata
from ...interfaces.bspline import TOPUPCoeffReorient
from ...interfaces.epi import GetReadoutTime, SortPEBlips
from ...interfaces.utils import PadSlices, ReorientImageAndMetadata, UniformGrid
from ...utils.misc import front as _front
from ..ancillary import init_brainextraction_wf

workflow = Workflow(name=name)
Expand All @@ -118,7 +117,7 @@ def init_topup_wf(
),
name="outputnode",
)
outputnode.inputs.method = "PEB/PEPOLAR (phase-encoding based / PE-POLARity)"
outputnode.inputs.method = _PEPOLAR_METHOD

# Calculate the total readout time of each run
readout_time = pe.MapNode(
Expand Down Expand Up @@ -238,13 +237,23 @@ def init_topup_wf(
return workflow


def init_3dQwarp_wf(omp_nthreads=1, debug=False, name="pepolar_estimate_wf"):
def init_3dQwarp_wf(
omp_nthreads=1,
debug=False,
sloppy=False,
name="pepolar_estimate_wf"):
"""
Create the PEPOLAR field estimation workflow based on AFNI's ``3dQwarp``.
This workflow takes in two EPI files that MUST have opposed
:abbr:`PE (phase-encoding)` direction.
Therefore, EPIs with orthogonal PE directions are not supported.
``3dQwarp`` is used to generate a displacement field and correct
the reference image. The workflow also returns an estimated fieldmap,
which is the result of converting the displacement field to a fieldmap
and then regularizing it with a bspline field. This means that the unwarped
image is in general not what one would get by reconstructing the fieldmap
from fmap_coeff and warping the in_data.
Workflow Graph
.. workflow ::
Expand All @@ -267,25 +276,46 @@ def init_3dQwarp_wf(omp_nthreads=1, debug=False, name="pepolar_estimate_wf"):
------
in_data : :obj:`list` of :obj:`str`
A list of two EPI files, the first of which will be taken as reference.
The reference PhaseEncodingDirection should match the value for
in_reference.
metadata : :obj:`list` of :obj:`dict`
A list with length matching the length of in_data. Each element should be a
dict with keys that are strings and values of any type. One key should be
PhaseEncodingDirection and the values should be BIDS-valid codings.
Outputs
-------
fmap : :obj:`str`
The path of the estimated fieldmap.
fmap_ref : :obj:`str`
The path of an unwarped conversion of the first element of ``in_data``.
The path of an unwarped conversion of files in ``in_data``.
fmap_mask : :obj:`str`
The path of mask corresponding to the ``fmap_ref`` output.
fmap_coeff : :obj:`str` or :obj:`list` of :obj:`str`
The path(s) of the B-Spline coefficients supporting the fieldmap.
method: :obj:`str`
Short description of the estimation method that was run.
out_warps: :obj:`str`
The displacement field from 3dQwarp, in ANTS format.
"""
from nipype.interfaces import afni
from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf
from niworkflows.interfaces.fixes import FixHeaderRegistration as Registration
from niworkflows.interfaces.freesurfer import StructuralReference
from niworkflows.interfaces.header import CopyHeader
from niworkflows.interfaces.fixes import (
FixHeaderRegistration as Registration,
FixHeaderApplyTransforms as ApplyTransforms,

from ...interfaces.bspline import (
DEFAULT_HF_ZOOMS_MM,
DEFAULT_ZOOMS_MM,
ApplyCoeffsField,
BSplineApprox,
)
from niworkflows.interfaces.freesurfer import StructuralReference
from niworkflows.func.util import init_enhance_and_skullstrip_bold_wf
from ...utils.misc import front as _front, last as _last
from ...interfaces.utils import Flatten, ConvertWarp
from ...interfaces.epi import GetReadoutTime
from ...interfaces.fmap import DisplacementsField2Fieldmap
from ...interfaces.utils import ConvertWarp, Flatten
from ...utils.misc import front, last


workflow = Workflow(name=name)
workflow.__desc__ = f"""{_PEPOLAR_DESC} \
Expand All @@ -297,7 +327,22 @@ def init_3dQwarp_wf(omp_nthreads=1, debug=False, name="pepolar_estimate_wf"):
)

outputnode = pe.Node(
niu.IdentityInterface(fields=["fmap", "fmap_ref"]), name="outputnode"
niu.IdentityInterface(
fields=[
"fmap",
"fmap_ref",
"fmap_mask",
"fmap_coeff",
"method",
"out_warps"]),
name="outputnode"
)
outputnode.inputs.method = _PEPOLAR_METHOD

readout_time = pe.Node(
GetReadoutTime(),
name="readout_time",
run_without_submitting=True,
)

flatten = pe.Node(Flatten(), name="flatten")
Expand Down Expand Up @@ -355,14 +400,24 @@ def init_3dQwarp_wf(omp_nthreads=1, debug=False, name="pepolar_estimate_wf"):

cphdr_warp = pe.Node(CopyHeader(), name="cphdr_warp", mem_gb=0.01)

unwarp_reference = pe.Node(
ApplyTransforms(
dimension=3,
float=True,
interpolation="LanczosWindowedSinc",
),
name="unwarp_reference",
# Extract the corresponding fieldmap in Hz
extract_field = pe.Node(
DisplacementsField2Fieldmap(), name="extract_field"
)

# Regularize with B-Splines
bs_filter = pe.Node(
BSplineApprox(debug=debug, extrapolate=not debug),
name="bs_filter",
)
bs_filter.interface._always_run = debug
bs_filter.inputs.bs_spacing = (
[DEFAULT_HF_ZOOMS_MM] if not sloppy else [DEFAULT_ZOOMS_MM]
)
if sloppy:
bs_filter.inputs.zooms_min = 4.0

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unwarp = pe.Node(ApplyCoeffsField(), name="unwarp")

# fmt: off
workflow.connect([
Expand All @@ -371,20 +426,32 @@ def init_3dQwarp_wf(omp_nthreads=1, debug=False, name="pepolar_estimate_wf"):
(flatten, sort_pe, [("out_list", "inlist")]),
(sort_pe, qwarp, [("qwarp_args", "args")]),
(sort_pe, merge_pes, [("sorted", "in_files")]),
(merge_pes, pe0_wf, [(("out_file", _front), "inputnode.in_file")]),
(merge_pes, pe1_wf, [(("out_file", _last), "inputnode.in_file")]),
(merge_pes, pe0_wf, [(("out_file", front), "inputnode.in_file")]),
(merge_pes, pe1_wf, [(("out_file", last), "inputnode.in_file")]),
(pe0_wf, align_pes, [("outputnode.skull_stripped_file", "fixed_image")]),
(pe1_wf, align_pes, [("outputnode.skull_stripped_file", "moving_image")]),
(pe0_wf, qwarp, [("outputnode.skull_stripped_file", "in_file")]),
(align_pes, qwarp, [("warped_image", "base_file")]),
(inputnode, cphdr_warp, [(("in_data", _front), "hdr_file")]),
(inputnode, cphdr_warp, [(("in_data", front), "hdr_file")]),
(qwarp, cphdr_warp, [("source_warp", "in_file")]),
(cphdr_warp, to_ants, [("out_file", "in_file")]),
(to_ants, unwarp_reference, [("out_file", "transforms")]),
(inputnode, unwarp_reference, [("in_reference", "reference_image"),
("in_reference", "input_image")]),
(unwarp_reference, outputnode, [("output_image", "fmap_ref")]),
(to_ants, outputnode, [("out_file", "fmap")]),
(pe0_wf, extract_field, [("outputnode.skull_stripped_file", "epi")]),
(to_ants, extract_field, [("out_file", "transform")]),
(inputnode, readout_time, [(("metadata", front), "metadata")]),
(readout_time, extract_field, [("readout_time", "ro_time"),
("pe_direction", "pe_dir")]),
(pe1_wf, unwarp, [("outputnode.skull_stripped_file", "in_data")]),
(pe0_wf, bs_filter, [("outputnode.mask_file", "in_mask")]),
(extract_field, bs_filter, [("out_file", "in_data")]),
(bs_filter, unwarp, [("out_coeff", "in_coeff")]),
(readout_time, unwarp, [("readout_time", "ro_time"),
("pe_direction", "pe_dir")]),
(bs_filter, outputnode, [("out_coeff", "fmap_coeff")]),
(qwarp, outputnode, [("warped_source", "fmap_ref")]),
(unwarp, outputnode, [("out_field", "fmap")]),
(pe0_wf, outputnode, [("outputnode.mask_file", "fmap_mask")]),
(to_ants, outputnode, [("out_file", "out_warps")])

])
# fmt: on
return workflow
Expand Down
28 changes: 18 additions & 10 deletions sdcflows/workflows/fit/tests/test_pepolar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,13 +25,14 @@
import pytest
from nipype.pipeline import engine as pe

from ..pepolar import init_topup_wf
from ..pepolar import init_3dQwarp_wf, init_topup_wf


@pytest.mark.skipif(os.getenv("TRAVIS") == "true", reason="this is TravisCI")
@pytest.mark.skipif(os.getenv("GITHUB_ACTIONS") == "true", reason="this is GH Actions")
@pytest.mark.parametrize("ds", ("ds001771", "HCP101006"))
def test_topup_wf(tmpdir, bids_layouts, workdir, outdir, ds):
@pytest.mark.parametrize("workflow", ("topup", "3dQwarp"))
def test_pepolar_wf(tmpdir, bids_layouts, workdir, outdir, ds, workflow):
"""Test preparation workflow."""
layout = bids_layouts[ds]
epi_path = sorted(
Expand All @@ -40,17 +41,24 @@ def test_topup_wf(tmpdir, bids_layouts, workdir, outdir, ds):
)
in_data = [f.path for f in epi_path]

wf = pe.Workflow(name=f"topup_{ds}")
topup_wf = init_topup_wf(omp_nthreads=2, debug=True, sloppy=True)
wf = pe.Workflow(name=f"{workflow}_{ds}")
if workflow == "topup":
init_pepolar = init_topup_wf
elif workflow == "3dQwarp":
init_pepolar = init_3dQwarp_wf
else:
msg = f"Unknown workflow: {workflow}"
raise ValueError(msg)
pepolar_wf = init_pepolar(omp_nthreads=2, debug=True, sloppy=True)
metadata = [layout.get_metadata(f.path) for f in epi_path]

topup_wf.inputs.inputnode.in_data = in_data
topup_wf.inputs.inputnode.metadata = metadata
pepolar_wf.inputs.inputnode.in_data = in_data
pepolar_wf.inputs.inputnode.metadata = metadata

if outdir:
from ...outputs import init_fmap_derivatives_wf, init_fmap_reports_wf

outdir = outdir / "unittests" / f"topup_{ds}"
outdir = outdir / "unittests" / f"{workflow}_{ds}"
fmap_derivatives_wf = init_fmap_derivatives_wf(
output_dir=str(outdir),
write_coeff=True,
Expand All @@ -67,18 +75,18 @@ def test_topup_wf(tmpdir, bids_layouts, workdir, outdir, ds):

# fmt: off
wf.connect([
(topup_wf, fmap_reports_wf, [("outputnode.fmap", "inputnode.fieldmap"),
(pepolar_wf, fmap_reports_wf, [("outputnode.fmap", "inputnode.fieldmap"),
("outputnode.fmap_ref", "inputnode.fmap_ref"),
("outputnode.fmap_mask", "inputnode.fmap_mask")]),
(topup_wf, fmap_derivatives_wf, [
(pepolar_wf, fmap_derivatives_wf, [
("outputnode.fmap", "inputnode.fieldmap"),
("outputnode.fmap_ref", "inputnode.fmap_ref"),
("outputnode.fmap_coeff", "inputnode.fmap_coeff"),
]),
])
# fmt: on
else:
wf.add_nodes([topup_wf])
wf.add_nodes([pepolar_wf])

if workdir:
wf.base_dir = str(workdir)
Expand Down

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