Fixed the fieldcoeff issue and also removed the linear transforms that are added to the warps. These are unnecessry

Author: Thomas Nickson

nipype/workflows/fmri/fsl/preprocess.py

@@ -1140,7 +1140,7 @@ def create_reg_workflow(name='registration'):
     mean2anat = pe.Node(fsl.FLIRT(), name='mean2anat')
     mean2anat.inputs.dof = 6
     register.connect(inputnode, 'mean_image', mean2anat, 'in_file')
-    register.connect(inputnode, 'anatomical_image', mean2anat, 'reference')
+    register.connect(stripper, 'out_file', mean2anat, 'reference')
 
     """
     Now use bbr cost function to improve the transform
@@ -1169,6 +1169,7 @@ def create_reg_workflow(name='registration'):
     """
 
     anat2target_nonlinear = pe.Node(fsl.FNIRT(), name='anat2target_nonlinear')
+    anat2target_nonlinear.inputs.fieldcoeff_file=True
     register.connect(anat2target_affine, 'out_matrix_file',
                      anat2target_nonlinear, 'affine_file')
     anat2target_nonlinear.inputs.warp_resolution = (8, 8, 8)
@@ -1188,8 +1189,7 @@ def create_reg_workflow(name='registration'):
     warpmean = warp2anat.clone(name='warpmean')
     register.connect(warp2anat, 'out_file', warpmean, 'in_file')
     register.connect(inputnode, 'target_image', warpmean, 'ref_file')
-    register.connect(anat2target_affine, 'out_matrix_file', warpmean, 'premat')
-    register.connect(anat2target_nonlinear, 'field_file',
+    register.connect(anat2target_nonlinear, 'fieldcoeff_file',
                      warpmean, 'field_file')
 
     """
@@ -1206,8 +1206,7 @@ def create_reg_workflow(name='registration'):
     warpall = warpall2anat.clone(name='warpall')
     register.connect(warpall2anat, 'out_file', warpall, 'in_file')
     register.connect(inputnode, 'target_image', warpall, 'ref_file')
-    register.connect(anat2target_affine, 'out_matrix_file', warpall, 'premat')
-    register.connect(anat2target_nonlinear, 'field_file',
+    register.connect(anat2target_nonlinear, 'fieldcoeff_file',
                      warpall, 'field_file')
 
     """
@@ -1218,7 +1217,7 @@ def create_reg_workflow(name='registration'):
     register.connect(warpall, 'out_file', outputnode, 'transformed_files')
     register.connect(mean2anatbbr, 'out_matrix_file',
                      outputnode, 'func2anat_transform')
-    register.connect(anat2target_nonlinear, 'field_file',
+    register.connect(anat2target_nonlinear, 'fieldcoeff_file',
                      outputnode, 'anat2target_transform')
 
     return register