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ENH: Add index_mask_file input to ImageStats #3005

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Merged
merged 3 commits into from
Aug 30, 2019
Merged

ENH: Add index_mask_file input to ImageStats #3005

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01fa94e
Add index_mask_file input to ImageStats
pndni-builder Aug 20, 2019
ac54739
add new autogenerated test file
pndni-builder Aug 21, 2019
22efaf7
add index_mask_file desc
stilley2 Aug 22, 2019
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5 changes: 5 additions & 0 deletions .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -695,6 +695,11 @@
"affiliation": "MIT, HMS",
"name": "Ghosh, Satrajit",
"orcid": "0000-0002-5312-6729"
},
{
"affiliation": "Holland Bloorview Kids Rehabilitation Hospital",
"name": "Tilley II, Steven",
"orcid": "0000-0003-4853-5082"
}
],
"keywords": [
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7 changes: 6 additions & 1 deletion nipype/interfaces/fsl/tests/test_auto_ImageStats.py
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Expand Up @@ -14,6 +14,11 @@ def test_ImageStats_inputs():
argstr='%s',
extensions=None,
mandatory=True,
position=3,
),
index_mask_file=dict(
argstr='-K %s',
extensions=None,
position=2,
),
mask_file=dict(
Expand All @@ -23,7 +28,7 @@ def test_ImageStats_inputs():
op_string=dict(
argstr='%s',
mandatory=True,
position=3,
position=4,
),
output_type=dict(),
split_4d=dict(
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11 changes: 9 additions & 2 deletions nipype/interfaces/fsl/utils.py
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Expand Up @@ -725,18 +725,25 @@ class ImageStatsInputSpec(FSLCommandInputSpec):
exists=True,
argstr="%s",
mandatory=True,
position=2,
position=3,
desc='input file to generate stats of')
op_string = traits.Str(
argstr="%s",
mandatory=True,
position=3,
position=4,
desc=("string defining the operation, options are "
"applied in order, e.g. -M -l 10 -M will "
"report the non-zero mean, apply a threshold "
"and then report the new nonzero mean"))
mask_file = File(
exists=True, argstr="", desc='mask file used for option -k %s')
index_mask_file = File(
exists=True,
argstr="-K %s",
position=2,
desc="generate seperate n submasks from indexMask, "
"for indexvalues 1..n where n is the maximum index "
"value in indexMask, and generate statistics for each submask")


class ImageStatsOutputSpec(TraitedSpec):
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