Merge pull request #2149 from salma1601/afni_allineate

ENH: add more inputs to AFNI 3dAllineate interface

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -313,7 +313,7 @@ class AllineateInputSpec(AFNICommandInputSpec):
         desc='Use a two pass alignment strategy for all volumes, searching '
              'for a large rotation+shift and then refining the alignment.')
     two_blur = traits.Float(
-        argstr='-twoblur',
+        argstr='-twoblur %f',
         desc='Set the blurring radius for the first pass in mm.')
     two_first = traits.Bool(
         argstr='-twofirst',
@@ -392,6 +392,18 @@ class AllineateInputSpec(AFNICommandInputSpec):
              'EPI slices, and the base as comprising anatomically '
              '\'true\' images.  Only phase-encoding direction image '
              'shearing and scaling will be allowed with this option.')
+    maxrot = traits.Float(
+        argstr='-maxrot %f',
+        desc='Maximum allowed rotation in degrees.')
+    maxshf = traits.Float(
+        argstr='-maxshf %f',
+        desc='Maximum allowed shift in mm.')
+    maxscl = traits.Float(
+        argstr='-maxscl %f',
+        desc='Maximum allowed scaling factor.')
+    maxshr = traits.Float(
+        argstr='-maxshr %f',
+        desc='Maximum allowed shearing factor.')
     master = File(
         exists=True,
         argstr='-master %s',

nipype/interfaces/afni/tests/test_auto_Allineate.py

@@ -51,6 +51,14 @@ def test_Allineate_inputs():
     ),
     master=dict(argstr='-master %s',
     ),
+    maxrot=dict(argstr='-maxrot %f',
+    ),
+    maxscl=dict(argstr='-maxscl %f',
+    ),
+    maxshf=dict(argstr='-maxshf %f',
+    ),
+    maxshr=dict(argstr='-maxshr %f',
+    ),
     newgrid=dict(argstr='-newgrid %f',
     ),
     nmatch=dict(argstr='-nmatch %d',
@@ -97,7 +105,7 @@ def test_Allineate_inputs():
     ),
     two_best=dict(argstr='-twobest %d',
     ),
-    two_blur=dict(argstr='-twoblur',
+    two_blur=dict(argstr='-twoblur %f',
     ),
     two_first=dict(argstr='-twofirst',
     ),