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FIX: Do not reorient magnitude images #98

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Apr 15, 2020
Merged

FIX: Do not reorient magnitude images #98

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fc4009b
FIX: Do not reorient magnitude images
effigies Apr 15, 2020
c15234e
DOC: Require Sphinx <3
effigies Apr 15, 2020
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4 changes: 2 additions & 2 deletions docs/requirements.txt
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Expand Up @@ -8,7 +8,7 @@ packaging
pydot>=1.2.3
pydotplus
sphinx-argparse
sphinx>=2.1.2
sphinx>=2.1.2,<3
sphinx_rtd_theme
sphinxcontrib-apidoc ~= 0.3.0
templateflow
templateflow
3 changes: 2 additions & 1 deletion sdcflows/workflows/gre.py
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Expand Up @@ -65,7 +65,8 @@ def init_magnitude_wf(omp_nthreads, name='magnitude_wf'):
name='outputnode')

# Merge input magnitude images
magmrg = pe.Node(IntraModalMerge(hmc=False), name='magmrg')
# Do not reorient to RAS to preserve the validity of PhaseEncodingDirection
magmrg = pe.Node(IntraModalMerge(hmc=False, to_ras=False), name='magmrg')

# de-gradient the fields ("bias/illumination artifact")
n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True),
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -42,7 +42,7 @@ include_package_data = True

[options.extras_require]
doc =
sphinx >= 2.1.2
sphinx >= 2.1.2, <3
pydot >= 1.2.3
pydotplus
sphinx_rtd_theme
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