@@ -420,10 +420,10 @@ def _run_interface(self, runtime):
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header = imgseries .header )
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mask_images = [img ]
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- nvols = self .inputs .ignore_initial_volumes
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- if nvols :
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+ skip_vols = self .inputs .ignore_initial_volumes
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+ if skip_vols :
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imgseries = imgseries .__class__ (
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- img .series .get_data ()[..., nvols :], imgseries .affine ,
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+ img .series .get_data ()[..., skip_vols :], imgseries .affine ,
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imgseries .header )
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mask_images = self ._process_masks (mask_images , imgseries .get_data ())
@@ -450,15 +450,15 @@ def _run_interface(self, runtime):
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imgseries .get_data (), mask_images , self .inputs .num_components ,
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self .inputs .pre_filter , degree , self .inputs .high_pass_cutoff , TR )
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- if nvols :
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+ if skip_vols :
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old_comp , old_basis = components , filter_basis
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- nrows = nvols + components .shape [0 ]
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+ nrows = skip_vols + components .shape [0 ]
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components = np .zeros ((nrows , components .shape [1 ]),
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dtype = components .dtype )
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- components [nvols :] = old_comp
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+ components [skip_vols :] = old_comp
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filter_basis = np .zeros ((nrows , filter_basis .shape [1 ]),
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dtype = filter_basis .dtype )
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- filter_basis [nvols :] = old_basis
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+ filter_basis [skip_vols :] = old_basis
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components_file = os .path .join (os .getcwd (), self .inputs .components_file )
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np .savetxt (components_file , components , fmt = b"%.10f" , delimiter = '\t ' ,
@@ -470,12 +470,12 @@ def _run_interface(self, runtime):
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'cosine' : 'cos' }[self .inputs .pre_filter ]
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ncols = filter_basis .shape [1 ] if filter_basis .size > 0 else 0
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header = ['{}{:02d}' .format (ftype , i ) for i in range (ncols )]
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- if nvols :
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- ss_col = np .zeros (( components .shape [0 ], 1 ) ,
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- dtype = filter_basis .dtype )
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- ss_col [: nvols ] = 1
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- filter_basis = np . hstack (( filter_basis , ss_col ) )
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- header . append ( 'SteadyState' )
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+ if skip_vols :
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+ ss_cols = np .eye ( components .shape [0 ], skip_vols ,
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+ dtype = filter_basis .dtype )
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+ filter_basis = np . hstack (( filter_basis , ss_cols ))
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+ header . extend ([ 'SteadyState{:02d}' . format ( i )
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+ for i in range ( skip_vols )] )
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np .savetxt (pre_filter_file , filter_basis , fmt = b'%.10f' ,
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delimiter = '\t ' , header = '\t ' .join (header ), comments = '' )
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