fix: test stripped brain image for FLIRT

Author: satra

examples/fmri_openfmri.py

@@ -305,6 +305,7 @@ def num_copes(files):
  wf.connect(preproc, 'outputspec.mean', registration, 'inputspec.mean_image')
  wf.connect(datasource, 'anat', registration, 'inputspec.anatomical_image')
  registration.inputs.inputspec.target_image = fsl.Info.standard_image('MNI152_T1_2mm.nii.gz')
+ registration.inputs.inputspec.target_image_brain = fsl.Info.standard_image('MNI152_T1_2mm_brain.nii.gz')
 
  def merge_files(copes, varcopes):
  out_files = []

nipype/workflows/fmri/fsl/preprocess.py

@@ -1104,7 +1104,8 @@ def create_reg_workflow(name='registration'):
  inputnode = pe.Node(interface=util.IdentityInterface(fields=['source_files',
  'mean_image',
  'anatomical_image',
- 'target_image']),
+ 'target_image',
+ 'target_image_brain']),
  name='inputspec')
  outputnode = pe.Node(interface=util.IdentityInterface(fields=['func2anat_transform',
  'anat2target_transform',
@@ -1161,8 +1162,11 @@ def create_reg_workflow(name='registration'):
  """
 
  anat2target_affine = pe.Node(fsl.FLIRT(), name='anat2target_linear')
- register.connect(inputnode, 'anatomical_image', anat2target_affine, 'in_file')
- register.connect(inputnode, 'target_image', anat2target_affine, 'reference')
+ anat2target.inputs.searchr_x = [-180, 180]
+ anat2target.inputs.searchr_y = [-180, 180]
+ anat2target.inputs.searchr_z = [-180, 180]
+ register.connect(stripper, 'out_file', anat2target_affine, 'in_file')
+ register.connect(inputnode, 'target_image_brain', anat2target_affine, 'reference')
 
  """
  Calculate nonlinear transform from anatomical to target