Merge pull request #1128 from blakedewey/master

Add -newgrid option to Warp interface

Author: satra

CHANGES

@@ -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)
 ============

nipype/interfaces/afni/preprocess.py

@@ -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")
@@ -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'
 
     """
 

nipype/interfaces/afni/tests/test_auto_Warp.py

@@ -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',