Merge pull request #2256 from salma1601/afni_Qwarp_allineate_option

allow allineate in Afni Qwarp

Author: satra

nipype/interfaces/afni/preprocess.py

@@ -2929,6 +2929,17 @@ class QwarpInputSpec(AFNICommandInputSpec):
  '* You CAN use -resample with these 3dQwarp options:'
  '-plusminus -inilev -iniwarp -duplo',
  argstr='-resample')
+ allineate = traits.Bool(
+ desc='This option will make 3dQwarp run 3dAllineate first, to align '
+ 'the source dataset to the base with an affine transformation. '
+ 'It will then use that alignment as a starting point for the '
+ 'nonlinear warping.',
+ argstr='-allineate')
+ allineate_opts = traits.Str(
+ desc='add extra options to the 3dAllineate command to be run by '
+ '3dQwarp.',
+ argstr='-allineate_opts %s',
+ xand=['allineate'])
  nowarp = traits.Bool(
  desc='Do not save the _WARP file.',
  argstr='-nowarp')
@@ -3465,11 +3476,24 @@ class Qwarp(AFNICommand):
  >>> qwarp2.cmdline # doctest: +ALLOW_UNICODE
  '3dQwarp -base mni.nii -blur 0.0 2.0 -source structural.nii -inilev 7 -iniwarp Q25_warp+tlrc.HEAD -prefix Q11'
  >>> res2 = qwarp2.run() # doctest: +SKIP
- """
+ >>> res2 = qwarp2.run() # doctest: +SKIP
+ >>> qwarp3 = afni.Qwarp()
+ >>> qwarp3.inputs.in_file = 'structural.nii'
+ >>> qwarp3.inputs.base_file = 'mni.nii'
+ >>> qwarp3.inputs.allineate = True
+ >>> qwarp3.inputs.allineate_opts = '-cose lpa -verb'
+ >>> qwarp3.cmdline # doctest: +ALLOW_UNICODE
+ "3dQwarp -allineate -allineate_opts '-cose lpa -verb' -base mni.nii -source structural.nii -prefix structural_QW"
+ >>> res3 = qwarp3.run() # doctest: +SKIP """
  _cmd = '3dQwarp'
  input_spec = QwarpInputSpec
  output_spec = QwarpOutputSpec
 
+ def _format_arg(self, name, spec, value):
+ if name == 'allineate_opts':
+ return spec.argstr % ("'" + value + "'")
+ return super(Qwarp, self)._format_arg(name, spec, value)
+
  def _list_outputs(self):
  outputs = self.output_spec().get()
 

nipype/interfaces/afni/tests/test_auto_Qwarp.py

@@ -8,6 +8,11 @@ def test_Qwarp_inputs():
  ),
  Qonly=dict(argstr='-Qonly',
  ),
+ allineate=dict(argstr='-allineate',
+ ),
+ allineate_opts=dict(argstr='-allineate_opts %s',
+ xand=['allineate'],
+ ),
  allsave=dict(argstr='-allsave',
  xor=['nopadWARP', 'duplo', 'plusminus'],
  ),