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FIX: Hard-wire MNI152NLin2009cAsym as standard space for SDC-SyN #63

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merged 1 commit into from
Nov 27, 2019
Merged

FIX: Hard-wire MNI152NLin2009cAsym as standard space for SDC-SyN #63

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24 changes: 8 additions & 16 deletions sdcflows/workflows/syn.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@


"""
import pkg_resources as pkgr
from pkg_resources import resource_filename

from nipype import logging
from nipype.pipeline import engine as pe
Expand Down Expand Up @@ -74,8 +74,6 @@ def init_syn_sdc_wf(omp_nthreads, epi_pe=None,
reference image
in_reference_brain
skull-stripped reference image
template : str
Name of template targeted by ``template`` output space
t1w_brain
skull-stripped, bias-corrected structural image
std2anat_xfm
Expand Down Expand Up @@ -127,7 +125,7 @@ def init_syn_sdc_wf(omp_nthreads, epi_pe=None,
template [@fieldmapless3].
""".format(ants_ver=Registration().version or '<ver>')
inputnode = pe.Node(
niu.IdentityInterface(['in_reference', 'in_reference_brain', 'template',
niu.IdentityInterface(['in_reference', 'in_reference_brain',
't1w_brain', 'std2anat_xfm']),
name='inputnode')
outputnode = pe.Node(
Expand All @@ -137,10 +135,10 @@ def init_syn_sdc_wf(omp_nthreads, epi_pe=None,

# Collect predefined data
# Atlas image and registration affine
atlas_img = pkgr.resource_filename('sdcflows', 'data/fmap_atlas.nii.gz')
atlas_img = resource_filename('sdcflows', 'data/fmap_atlas.nii.gz')
# Registration specifications
affine_transform = pkgr.resource_filename('sdcflows', 'data/affine.json')
syn_transform = pkgr.resource_filename('sdcflows', 'data/susceptibility_syn.json')
affine_transform = resource_filename('sdcflows', 'data/affine.json')
syn_transform = resource_filename('sdcflows', 'data/susceptibility_syn.json')

invert_t1w = pe.Node(Rescale(invert=True), name='invert_t1w',
mem_gb=0.3)
Expand All @@ -153,6 +151,8 @@ def init_syn_sdc_wf(omp_nthreads, epi_pe=None,
# 1) BOLD -> T1; 2) MNI -> T1; 3) ATLAS -> MNI
transform_list = pe.Node(niu.Merge(3), name='transform_list',
mem_gb=DEFAULT_MEMORY_MIN_GB)
transform_list.inputs.in3 = resource_filename(
'sdcflows', 'data/fmap_atlas_2_MNI152NLin2009cAsym_affine.mat')
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In reality, we only have this pre-calculated affine, so offering to switch was asking for trouble.


# Inverting (1), then applying in reverse order:
#
Expand Down Expand Up @@ -193,8 +193,7 @@ def init_syn_sdc_wf(omp_nthreads, epi_pe=None,
(ref_2_t1, t1_2_ref, [('forward_transforms', 'transforms')]),
(ref_2_t1, transform_list, [('forward_transforms', 'in1')]),
(inputnode, transform_list, [
('std2anat_xfm', 'in2'),
(('template', _prior_path), 'in3')]),
('std2anat_xfm', 'in2')]),
(inputnode, atlas_2_ref, [('in_reference', 'reference_image')]),
(transform_list, atlas_2_ref, [('out', 'transforms')]),
(atlas_2_ref, threshold_atlas, [('output_image', 'in_file')]),
Expand All @@ -215,10 +214,3 @@ def init_syn_sdc_wf(omp_nthreads, epi_pe=None,
])

return workflow


def _prior_path(template):
"""Select an appropriate input xform, based on template."""
from pkg_resources import resource_filename
return resource_filename(
'sdcflows', 'data/fmap_atlas_2_{}_affine.mat'.format(template))
5 changes: 2 additions & 3 deletions setup.cfg
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Expand Up @@ -25,9 +25,8 @@ setup_requires =
install_requires =
nibabel >=2.2.1
niflow-nipype1-workflows ~= 0.0.1
nipype ~= 1.3.0
# nipype @ git+https://github.com/nipy/nipype.git@5058ab7dfa6c32d4f3a16ee698a8fc4e3d28bee7
niworkflows ~= 1.0.0rc1
nipype >= 1.3.1
niworkflows ~= 1.0.0
numpy
pybids ~=0.9.2
templateflow ~= 0.4
Expand Down