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Add -newgrid option to Warp interface #1128

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Merged
merged 4 commits into from
Jul 6, 2015
Merged

Add -newgrid option to Warp interface #1128

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c17758a
Added -newgrid option to Warp interface in AFNI (3dWarp wrapper)
blakedewey Jul 6, 2015
51ddd8f
Merge pull request #4 from nipy/master
blakedewey Jul 6, 2015
7a66fdd
Updated CHANGES
blakedewey Jul 6, 2015
a0aa398
Merge remote-tracking branch 'origin/master'
blakedewey Jul 6, 2015
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1 change: 1 addition & 0 deletions CHANGES
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ Next release
* FIX: SSHDataGrabber outputs now return full path to the grabbed/downloaded files. (https://github.com/nipy/nipype/pull/1086)
* FIX: Add QA output for TSNR to resting workflow (https://github.com/nipy/nipype/pull/1088)
* FIX: Change N4BiasFieldCorrection to use short tag for dimensionality (backward compatible) (https://github.com/nipy/nipype/pull/1096)
* ENH: Added -newgrid input to Warp in AFNI (3dWarp wrapper) (https://github.com/nipy/nipype/pull/1128)

Release 0.10.0 (October 10, 2014)
============
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11 changes: 10 additions & 1 deletion nipype/interfaces/afni/preprocess.py
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Expand Up @@ -233,6 +233,9 @@ class WarpInputSpec(AFNICommandInputSpec):
argstr="-gridset %s",
exists=True)

newgrid = traits.Float(desc="specify grid of this size (mm)",
argstr="-newgrid %f")

zpad = traits.Int(desc="pad input dataset with N planes" +
" of zero on all sides.",
argstr="-zpad %d")
Expand All @@ -254,7 +257,13 @@ class Warp(AFNICommand):
>>> warp.inputs.out_file = "trans.nii.gz"
>>> warp.cmdline
'3dWarp -deoblique -prefix trans.nii.gz structural.nii'
>>> res = warp.run() # doctest: +SKIP

>>> warp_2 = afni.Warp()
>>> warp_2.inputs.in_file = 'structural.nii'
>>> warp_2.inputs.newgrid = 1.0
>>> warp_2.inputs.out_file = "trans.nii.gz"
>>> warp_2.cmdline
'3dWarp -newgrid 1.000000 -prefix trans.nii.gz structural.nii'

"""

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2 changes: 2 additions & 0 deletions nipype/interfaces/afni/tests/test_auto_Warp.py
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Expand Up @@ -26,6 +26,8 @@ def test_Warp_inputs():
),
mni2tta=dict(argstr='-mni2tta',
),
newgrid=dict(argstr='-newgrid %f',
),
out_file=dict(argstr='-prefix %s',
name_source='in_file',
name_template='%s_warp',
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