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[ENH] Respect SliceEncodingDirection metadata #1350

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Merged
merged 7 commits into from
Nov 1, 2018
Merged

[ENH] Respect SliceEncodingDirection metadata #1350

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6d3138f
added SliceEncodingDirection to stc
fliem Oct 25, 2018
f9b2778
updated zenodo file
fliem Oct 25, 2018
1dd2270
Merge branch 'master' into fix-stc
oesteban Oct 26, 2018
f9baab8
updated reqs to nipype>=1.1.4
fliem Nov 1, 2018
7ed02c9
removed empty line
fliem Nov 1, 2018
ff2796f
moved slice_encoding_direction input
fliem Nov 1, 2018
9fdf78c
Merge remote-tracking branch 'upstream/master' into fix-stc
effigies Nov 1, 2018
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5 changes: 5 additions & 0 deletions .zenodo.json
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Expand Up @@ -83,6 +83,11 @@
"affiliation": "Department of Psychology, University of Oslo",
"orcid": "0000-0002-8508-9088"
},
{
"name": "Liem, Franz",
"affiliation": "University of Zurich",
"orcid": "0000-0003-0646-4810"
},
{
"name": "Poldrack, Russell A.",
"affiliation": "Department of Psychology, Stanford University",
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2 changes: 1 addition & 1 deletion fmriprep/__about__.py
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Expand Up @@ -97,7 +97,7 @@
'grabbit==0.2.3',
'pybids==0.6.5',
'nitime',
'nipype>=1.1.3',
'nipype>=1.1.4',
'niworkflows==0.4.4',
'statsmodels',
'seaborn',
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2 changes: 2 additions & 0 deletions fmriprep/workflows/bold/stc.py
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Expand Up @@ -71,6 +71,8 @@ def init_bold_stc_wf(metadata, name='bold_stc_wf'):
tr='{}s'.format(metadata["RepetitionTime"]),
slice_timing=metadata['SliceTiming']),
name='slice_timing_correction')
if 'SliceEncodingDirection' in metadata:
slice_timing_correction.inputs.slice_encoding_direction = metadata['SliceEncodingDirection']
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@effigies effigies Nov 1, 2018

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Maybe we could be as clear (and not hit line length limits) by just adding slice_encoding_direction=metadata.get('SliceEncodingDirection', 'k') to the TShift() call.

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@fliem fliem Nov 1, 2018

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OK. I have tested the previous version and this looks good

  • same list order, different direction gives different results (as expected)
  • flipped list, flipped direction gives same results (as expected)
  • no direction vs "k" gives same results (as expected)


copy_xform = pe.Node(CopyXForm(), name='copy_xform', mem_gb=0.1)

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