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FIX: DTITK nonlinear workflow origin reslicing #2561

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Merged
merged 10 commits into from
May 24, 2018
Merged

FIX: DTITK nonlinear workflow origin reslicing #2561

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284f0dd
Merge branch 'master' of https://github.com/nipy/nipype
kesshijordan Apr 10, 2018
ebe82a4
Merge branch 'master' of https://github.com/nipy/nipype
kesshijordan Apr 16, 2018
6db39fd
Merge branch 'master' of https://github.com/nipy/nipype
kesshijordan Apr 29, 2018
5407f0a
moved origins to zero prior to any reslicing (this avoids a problem p…
kesshijordan Apr 29, 2018
ac3286d
reslice output image to match input fixed
kesshijordan May 16, 2018
5d238c0
added apply_xfm workflow
kesshijordan May 23, 2018
73abfda
nonlinear wf works with nonzero origin images
kesshijordan May 23, 2018
5037c40
Merge branch 'master' of https://github.com/kesshijordan/nipype into …
kesshijordan May 24, 2018
fe3c97e
specs
kesshijordan May 24, 2018
9545859
removed non-functional wf
kesshijordan May 24, 2018
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moved origins to zero prior to any reslicing (this avoids a problem p… 
…resent in some images where the volume gets truncated upon reslicing)
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@kesshijordan
kesshijordan committed Apr 29, 2018
commit 5407f0a2dbf35beff8d694bf8e416a4cb40cb3da
10 changes: 7 additions & 3 deletions nipype/workflows/dmri/dtitk/tensor_registration.py
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Expand Up @@ -75,7 +75,9 @@ def diffeomorphic_tensor_pipeline(name='DiffeoTen',
fields=['out_file', 'out_file_xfm',
'fixed_resliced', 'moving_resliced']),
name='outputnode')

origin_node_fixed = pe.Node(dtitk.TVAdjustVoxSp(origin=(0, 0, 0)),
name='origin_node_fixed')
origin_node_moving = origin_node_fixed.clone(name='origin_node_moving')
reslice_node_pow2 = pe.Node(dtitk.TVResample(
origin=(0, 0, 0),
array_size=params['array_size']),
Expand All @@ -96,10 +98,12 @@ def diffeomorphic_tensor_pipeline(name='DiffeoTen',
wf = pe.Workflow(name=name)

# Reslice input images
wf.connect(inputnode, 'fixed_file', reslice_node_pow2, 'in_file')
wf.connect(inputnode, 'fixed_file', origin_node_fixed, 'in_file')
wf.connect(origin_node_fixed, 'out_file', reslice_node_pow2, 'in_file')
wf.connect(reslice_node_pow2, 'out_file',
reslice_node_moving, 'target_file')
wf.connect(inputnode, 'moving_file', reslice_node_moving, 'in_file')
wf.connect(inputnode, 'moving_file', origin_node_moving, 'in_file')
wf.connect(origin_node_moving, 'out_file', reslice_node_moving, 'in_file')
# Rigid registration
wf.connect(reslice_node_pow2, 'out_file', rigid_node, 'fixed_file')
wf.connect(reslice_node_moving, 'out_file', rigid_node, 'moving_file')
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