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FIX: Normalize phase-encoding polarity of coefficients after TOPUP #202

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Merged
merged 1 commit into from
May 6, 2021
Merged

FIX: Normalize phase-encoding polarity of coefficients after TOPUP #202

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22 changes: 18 additions & 4 deletions sdcflows/interfaces/bspline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -327,7 +327,18 @@ class _TOPUPCoeffReorientInputSpec(BaseInterfaceInputSpec):
File(exist=True), mandatory=True, desc="input coefficients file(s) from TOPUP"
)
fmap_ref = File(exists=True, mandatory=True, desc="the fieldmap reference")

pe_dir = traits.Enum(
"+",
"-",
"i",
"i-",
"j",
"j-",
"k",
"k-",
usedefault=True,
desc="the polarity of the phase-encoding direction corresponding to fmap_ref",
)

class _TOPUPCoeffReorientOutputSpec(TraitedSpec):
out_coeff = OutputMultiObject(File(exists=True), desc="patched coefficients")
Expand Down Expand Up @@ -368,7 +379,8 @@ def _run_interface(self, runtime):
_fix_topup_fieldcoeff(
in_coeff,
self.inputs.fmap_ref,
fname_presuffix(in_coeff, suffix="_fixed", newpath=runtime.cwd),
refpe_reversed=self.inputs.pe_dir.endswith("-"),
out_file=fname_presuffix(in_coeff, suffix="_fixed", newpath=runtime.cwd),
)
)
for in_coeff in self.inputs.in_coeff
Expand Down Expand Up @@ -598,7 +610,7 @@ def _move_coeff(in_coeff, fmap_ref, transform):
return out


def _fix_topup_fieldcoeff(in_coeff, fmap_ref, out_file=None):
def _fix_topup_fieldcoeff(in_coeff, fmap_ref, refpe_reversed=False, out_file=None):
"""Read in a coefficients file generated by TOPUP and fix x-form headers."""
from pathlib import Path
import numpy as np
Expand Down Expand Up @@ -627,5 +639,7 @@ def _fix_topup_fieldcoeff(in_coeff, fmap_ref, out_file=None):
coeffnii.header.set_qform(coeffnii.header.get_qform(coded=False), code=0)
coeffnii.header.set_sform(newaff, code=1)

coeffnii.__class__(coeffnii.dataobj, newaff, header).to_filename(out_file)
# If the reference is reversed encoded, flip the displacements
coeffs = (1.0 - 2.0 * refpe_reversed) * np.asanyarray(coeffnii.dataobj)
coeffnii.__class__(coeffs, newaff, header).to_filename(out_file)
return out_file
11 changes: 9 additions & 2 deletions sdcflows/workflows/fit/pepolar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -72,6 +72,7 @@ def init_topup_wf(omp_nthreads=1, sloppy=False, debug=False, name="pepolar_estim
from niworkflows.interfaces.nibabel import MergeSeries
from niworkflows.interfaces.images import IntraModalMerge

from ...utils.misc import front as _front
from ...interfaces.epi import GetReadoutTime
from ...interfaces.utils import Flatten
from ...interfaces.bspline import TOPUPCoeffReorient
Expand Down Expand Up @@ -125,6 +126,11 @@ def init_topup_wf(omp_nthreads=1, sloppy=False, debug=False, name="pepolar_estim

brainextraction_wf = init_brainextraction_wf()

def _getpe(in_meta):
if isinstance(in_meta, list):
in_meta = in_meta[0]
return in_meta["PhaseEncodingDirection"]

# fmt: off
workflow.connect([
(inputnode, flatten, [("in_data", "in_data"),
Expand All @@ -135,9 +141,10 @@ def init_topup_wf(omp_nthreads=1, sloppy=False, debug=False, name="pepolar_estim
(flatten, topup, [(("out_meta", _pe2fsl), "encoding_direction")]),
(readout_time, topup, [("readout_time", "readout_times")]),
(concat_blips, topup, [("out_file", "in_file")]),
(flatten, fix_coeff, [(("out_data", _front), "fmap_ref"),
(("out_meta", _getpe), "pe_dir")]),
(topup, fix_coeff, [("out_fieldcoef", "in_coeff")]),
(topup, merge_corrected, [("out_corrected", "in_files")]),
(topup, fix_coeff, [("out_fieldcoef", "in_coeff"),
("out_corrected", "fmap_ref")]),
(topup, outputnode, [("out_field", "fmap"),
("out_jacs", "jacobians"),
("out_mats", "xfms"),
Expand Down