apply inverse coreg matrix to tissue mask conversions to func space for nuisance

Author: HechengJin0

CPAC/nuisance/utils/__init__.py

@@ -317,18 +317,29 @@ def generate_summarize_tissue_mask(nuisance_wf,
             pass
 
         elif step == 'resolution':
-
             mask_to_epi = pe.Node(interface=fsl.FLIRT(),
                                   name='{}_flirt'
                                        .format(node_mask_key))
 
             mask_to_epi.inputs.interp = 'nearestneighbour'
 
             if regressor_selector['extraction_resolution'] == "Functional":
+                # invert func2anat matrix to get anat2func_linear_xfm
+                anat2func_linear_xfm = pe.Node(interface=fsl.ConvertXFM(), name='anat2func_linear_xfm')
+                anat2func_linear_xfm.inputs.invert_xfm = True
+                nuisance_wf.connect(*(
+                    pipeline_resource_pool['Transformations']['func_to_anat_linear_xfm'] + 
+                    (anat2func_linear_xfm, 'in_file')
+                ))
+                # apply anat2func matrix
+                mask_to_epi.inputs.apply_xfm = True
+                mask_to_epi.inputs.output_type = 'NIFTI_GZ'
                 nuisance_wf.connect(*(
                     pipeline_resource_pool['Functional_mean'] +
                     (mask_to_epi, 'reference')
                 ))
+                nuisance_wf.connect(anat2func_linear_xfm, 'out_file', 
+                                    mask_to_epi, 'in_matrix_file')
             else:
                 resolution = regressor_selector['extraction_resolution']
                 mask_to_epi.inputs.apply_isoxfm = resolution