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FIX: fix for some missed DTIs during dcm2niix conversion #2110

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Merged
merged 1 commit into from
Jul 6, 2017

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leej3
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@leej3 leej3 commented Jul 5, 2017

Fixes #2109.

Changes proposed in this pull request

  • Add an extra term to search for in the dcm2niix stdout to detect for these dicoms.

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codecov-io commented Jul 6, 2017

Codecov Report

Merging #2110 into master will increase coverage by 23.59%.
The diff coverage is 0%.

Impacted file tree graph

@@             Coverage Diff             @@
##           master    #2110       +/-   ##
===========================================
+ Coverage   48.56%   72.16%   +23.59%     
===========================================
  Files         116     1144     +1028     
  Lines       23598    57606    +34008     
  Branches        0     8251     +8251     
===========================================
+ Hits        11461    41572    +30111     
- Misses      12137    14733     +2596     
- Partials        0     1301     +1301
Flag Coverage Δ
#smoketests 72.16% <0%> (+23.59%) ⬆️
#unittests 69.79% <0%> (?)
Impacted Files Coverage Δ
nipype/interfaces/dcm2nii.py 43.06% <0%> (ø)
...rfaces/spm/tests/test_auto_TwoSampleTTestDesign.py 85.71% <0%> (ø)
...pype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py 85.71% <0%> (ø)
...rfaces/dipy/tests/test_auto_SimulateMultiTensor.py 85.71% <0%> (ø)
...pipeline/plugins/tests/test_multiproc_nondaemon.py 53.52% <0%> (ø)
nipype/interfaces/niftyseg/label_fusion.py 57.46% <0%> (ø)
nipype/algorithms/tests/test_icc_anova.py 100% <0%> (ø)
.../brains/tests/test_auto_HistogramMatchingFilter.py 85.71% <0%> (ø)
...sts/test_auto_MultiResolutionAffineRegistration.py 85.71% <0%> (ø)
...faces/semtools/tests/test_auto_DWISimpleCompare.py 78.57% <0%> (ø)
... and 1084 more

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@@ -304,7 +304,7 @@ def _parse_stdout(self, stdout):
bvals.append(out_file + ".bval")
find_b = False
# next scan will have bvals/bvecs
elif 'DTI gradients' in line or 'DTI gradient directions' in line:
elif 'DTI gradients' in line or 'DTI gradient directions' in line or 'DTI vectors' in line:
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@leej3 - i'm going to merge this in, but it would be good to submit an issue to dcm2niix to make this string uniform across scanners/dicoms.

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@satra - Good point. Didn't even think of that. Will do. Thanks.

@satra satra merged commit 2ee584b into nipy:master Jul 6, 2017
@satra satra added this to the 0.14.0 milestone Oct 20, 2017
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3 participants