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[RTM] RF: Use N4BiasFieldCorrection(copy_header=True) #542

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Merged
merged 4 commits into from
Jun 1, 2017
Merged

[RTM] RF: Use N4BiasFieldCorrection(copy_header=True) #542

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450c1bf
RF: Replace n4bias_wf with copy_header=True
effigies May 30, 2017
2b39c6e
RF: Use copy_header=True in phdiff
effigies May 30, 2017
05c1798
Update pins
effigies May 30, 2017
30ff1e9
FIX: Drop deprecated testing trait
effigies May 31, 2017
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4 changes: 2 additions & 2 deletions docs/environment.yml
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Expand Up @@ -28,6 +28,6 @@ dependencies:
- svgutils
- nitime
- nilearn
- git+https://github.com/nipy/nipype.git@c13f967506aa426c63ad4131cf29b655f742649c#egg=nipype
- git+https://github.com/poldracklab/niworkflows.git@0.0.7#egg=niworkflows
- git+https://github.com/nipy/nipype.git@603f424a379767abffa055283b799d69b840a58d#egg=nipype
- git+https://github.com/poldracklab/niworkflows.git@70a85b98e6161620af1763c050212e348cd20388#egg=niworkflows
- git+https://github.com/INCF/pybids.git@7205ae01fbdca8e8bfd26ac773b1134b84c8af0c#egg=pybids
2 changes: 1 addition & 1 deletion fmriprep/workflows/anatomical.py
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Expand Up @@ -81,7 +81,7 @@ def init_anat_preproc_wf(skull_strip_ants, output_spaces, template, debug, frees
RobustMNINormalizationRPT(
generate_report=True,
num_threads=omp_nthreads,
testing=debug,
flavor='testing' if debug else 'precise',
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@oesteban I believe this is the 0.0.7+ equivalent?

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yes

),
name='t1_2_mni'
)
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10 changes: 5 additions & 5 deletions fmriprep/workflows/fieldmap/fmap.py
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Expand Up @@ -21,10 +21,9 @@
from nipype.pipeline import engine as pe
from nipype.interfaces import utility as niu

from nipype.interfaces import fsl
from nipype.interfaces import fsl, ants
from niworkflows.interfaces.masks import BETRPT
from nipype.workflows.dmri.fsl.utils import demean_image, cleanup_edge_pipeline
from fmriprep.workflows.util import init_n4bias_wf
from fmriprep.interfaces import IntraModalMerge
from fmriprep.interfaces.bids import DerivativesDataSink
from fmriprep.interfaces.fmap import FieldEnhance
Expand Down Expand Up @@ -60,7 +59,8 @@ def init_fmap_wf(reportlets_dir, omp_nthreads, fmap_bspline, name='fmap_wf'):
name='fmapmrg')

# de-gradient the fields ("bias/illumination artifact")
n4bias_wf = init_n4bias_wf()
n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True),
name='n4_correct')
bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
name='bet')
ds_fmap_mask = pe.Node(
Expand All @@ -70,8 +70,8 @@ def init_fmap_wf(reportlets_dir, omp_nthreads, fmap_bspline, name='fmap_wf'):
workflow.connect([
(inputnode, magmrg, [('magnitude', 'in_files')]),
(inputnode, fmapmrg, [('fieldmap', 'in_files')]),
(magmrg, n4bias_wf, [('out_file', 'inputnode.in_file')]),
(n4bias_wf, bet, [('outputnode.out_file', 'in_file')]),
(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')]),
Expand Down
2 changes: 1 addition & 1 deletion fmriprep/workflows/fieldmap/phdiff.py
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Expand Up @@ -75,7 +75,7 @@ def _pick1st(inlist):
magmrg = pe.Node(IntraModalMerge(), name='magmrg')

# de-gradient the fields ("bias/illumination artifact")
n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='n4')
n4 = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True), name='n4')
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Note that this wasn't using init_n4bias_wf already. If there's a good reason for not copying the header, let me know and I'll revert this.

bet = pe.Node(BETRPT(generate_report=True, frac=0.6, mask=True),
name='bet')
ds_fmap_mask = pe.Node(
Expand Down
30 changes: 6 additions & 24 deletions fmriprep/workflows/util.py
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Expand Up @@ -13,7 +13,6 @@

import nipype.interfaces.fsl as fsl
import nipype.interfaces.afni as afni
from niworkflows.interfaces import CopyHeader
from niworkflows.interfaces.masks import SimpleShowMaskRPT


Expand All @@ -26,7 +25,8 @@ def init_enhance_and_skullstrip_epi_wf(name='enhance_and_skullstrip_epi_wf'):
'bias_corrected_file',
'out_report']),
name='outputnode')
n4bias_wf = init_n4bias_wf()
n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3, copy_header=True),
name='n4_correct')
skullstrip_first_pass = pe.Node(fsl.BET(frac=0.2, mask=True),
name='skullstrip_first_pass')
unifize = pe.Node(afni.Unifize(t2=True, outputtype='NIFTI_GZ',
Expand All @@ -42,38 +42,20 @@ def init_enhance_and_skullstrip_epi_wf(name='enhance_and_skullstrip_epi_wf'):
mask_reportlet = pe.Node(SimpleShowMaskRPT(), name='mask_reportlet')

workflow.connect([
(inputnode, n4bias_wf, [('in_file', 'inputnode.in_file')]),
(n4bias_wf, skullstrip_first_pass, [('outputnode.out_file', 'in_file')]),
(inputnode, n4_correct, [('in_file', 'input_image')]),
(n4_correct, skullstrip_first_pass, [('output_image', 'in_file')]),
(skullstrip_first_pass, unifize, [('out_file', 'in_file')]),
(unifize, skullstrip_second_pass, [('out_file', 'in_file')]),
(skullstrip_first_pass, combine_masks, [('mask_file', 'in_file')]),
(skullstrip_second_pass, combine_masks, [('out_file', 'operand_file')]),
(unifize, apply_mask, [('out_file', 'in_file')]),
(combine_masks, apply_mask, [('out_file', 'mask_file')]),
(n4bias_wf, mask_reportlet, [('outputnode.out_file', 'background_file')]),
(n4_correct, mask_reportlet, [('output_image', 'background_file')]),
(combine_masks, mask_reportlet, [('out_file', 'mask_file')]),
(combine_masks, outputnode, [('out_file', 'mask_file')]),
(mask_reportlet, outputnode, [('out_report', 'out_report')]),
(apply_mask, outputnode, [('out_file', 'skull_stripped_file')]),
(n4bias_wf, outputnode, [('outputnode.out_file', 'bias_corrected_file')]),
])

return workflow


def init_n4bias_wf(name='n4bias_wf'):
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')

n4_correct = pe.Node(ants.N4BiasFieldCorrection(dimension=3), name='n4_correct')
orig_hdr = pe.Node(CopyHeader(), name='orig_hdr')

workflow.connect([
(inputnode, n4_correct, [('in_file', 'input_image')]),
(inputnode, orig_hdr, [('in_file', 'hdr_file')]),
(n4_correct, orig_hdr, [('output_image', 'in_file')]),
(orig_hdr, outputnode, [('out_file', 'out_file')]),
(n4_correct, outputnode, [('output_image', 'bias_corrected_file')]),
])

return workflow
4 changes: 2 additions & 2 deletions requirements.txt
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@@ -1,3 +1,3 @@
git+https://github.com/nipy/nipype.git@c13f967506aa426c63ad4131cf29b655f742649c#egg=nipype
git+https://github.com/poldracklab/niworkflows.git@0.0.7#egg=niworkflows
git+https://github.com/nipy/nipype.git@603f424a379767abffa055283b799d69b840a58d#egg=nipype
git+https://github.com/poldracklab/niworkflows.git@70a85b98e6161620af1763c050212e348cd20388#egg=niworkflows
git+https://github.com/INCF/pybids.git@7205ae01fbdca8e8bfd26ac773b1134b84c8af0c#egg=pybids