👽 Update mask → mask_file for Nipype upgrade

Author: shnizzedy

CPAC/nuisance/nuisance.py

@@ -2,43 +2,30 @@
 import os
 import numpy as np
 import nibabel as nb
-
 import nipype.pipeline.engine as pe
 import nipype.interfaces.utility as util
-import nipype.interfaces.fsl as fsl
-import nipype.interfaces.ants as ants
-import nipype.interfaces.c3 as c3
+import CPAC
+
+from nipype.interfaces import fsl
+from nipype.interfaces import ants
+from nipype.interfaces import c3
 from nipype.interfaces import afni
 from nipype.interfaces.afni import utils as afni_utils
-
-import CPAC
-import CPAC.utils as utils
+from scipy.fftpack import fft, ifft
+from CPAC import utils
 from CPAC.utils.interfaces.function import Function
 from CPAC.utils.interfaces.masktool import MaskTool
 from CPAC.utils.interfaces.pc import PC
-
 from CPAC.nuisance.utils import (
     find_offending_time_points,
     generate_summarize_tissue_mask,
-    temporal_variance_mask,
-    calc_compcor_components
-)
-
+    temporal_variance_mask)
 from CPAC.nuisance.utils.compcor import (
     calc_compcor_components,
     cosine_filter,
     TR_string_to_float)
-
-
 from CPAC.utils.datasource import check_for_s3
-
-from scipy.fftpack import fft, ifft
-
 from .bandpass import bandpass_voxels
-import nipype.pipeline.engine as pe
-import nipype.interfaces.utility as util
-import nipype.interfaces.fsl as fsl
-import nipype.interfaces.ants as ants
 
 
 def gather_nuisance(functional_file_path,
@@ -1212,7 +1199,7 @@ def create_regressor_workflow(nuisance_selectors,
 
                         nuisance_wf.connect(
                             union_masks_paths, 'out_file',
-                            mean_node, 'mask'
+                            mean_node, 'mask_file'
                         )
 
                         summary_method_input = (mean_node, 'out_file')

CPAC/timeseries/timeseries_analysis.py

@@ -1,7 +1,8 @@
 import nipype.pipeline.engine as pe
-import nipype.interfaces.fsl as fsl
 import nipype.interfaces.utility as util
-import nipype.interfaces.afni as afni
+
+from nipype.interfaces import fsl
+from nipype.interfaces import afni
 from nipype import logging
 
 
@@ -248,7 +249,7 @@ def get_roi_timeseries(wf_name='roi_timeseries'):
                   timeseries_roi, 'in_file')
 
     wflow.connect(inputnode_roi, 'roi',
-                  timeseries_roi, 'mask')
+                  timeseries_roi, 'mask_file')
 
     clean_csv_imports = ['import os']
     clean_csv = pe.Node(util.Function(input_names=['roi_csv'],