@@ -192,7 +192,9 @@ class DWIBiasCorrectInputSpec(MRTrix3BaseInputSpec):
192192 mandatory = True ,
193193 desc = "input DWI image" ,
194194 )
195- in_mask = File (argstr = "-mask %s" , desc = "input mask image for bias field estimation" )
195+ in_mask = File (
196+ argstr = "-mask %s" , desc = "input mask image for bias field estimation"
197+ )
196198 use_ants = traits .Bool (
197199 argstr = "ants" ,
198200 mandatory = True ,
@@ -407,8 +409,10 @@ def _list_outputs(self):
407409 outputs = self .output_spec ().get ()
408410 outputs ["out_file" ] = op .abspath (self .inputs .out_file )
409411 if self .inputs .out_grad_mrtrix :
410- outputs ["out_grad_mrtrix" ] = op .abspath (self .inputs .out_grad_mrtrix )
411- if self .inputs .export_grad_fsl :
412+ outputs ["out_grad_mrtrix" ] = op .abspath (
413+ self .inputs .out_grad_mrtrix
414+ )
415+ if self .inputs .out_fsl_bvec :
412416 outputs ["out_fsl_bvec" ] = op .abspath (self .inputs .out_grad_fsl [0 ])
413417 outputs ["out_fsl_bval" ] = op .abspath (self .inputs .out_grad_fsl [1 ])
414418
@@ -441,9 +445,15 @@ class ResponseSDInputSpec(MRTrix3BaseInputSpec):
441445 usedefault = True ,
442446 desc = "output WM response text file" ,
443447 )
444- gm_file = File (argstr = "%s" , position = - 2 , desc = "output GM response text file" )
445- csf_file = File (argstr = "%s" , position = - 1 , desc = "output CSF response text file" )
446- in_mask = File (exists = True , argstr = "-mask %s" , desc = "provide initial mask image" )
448+ gm_file = File (
449+ argstr = "%s" , position = - 2 , desc = "output GM response text file"
450+ )
451+ csf_file = File (
452+ argstr = "%s" , position = - 1 , desc = "output CSF response text file"
453+ )
454+ in_mask = File (
455+ exists = True , argstr = "-mask %s" , desc = "provide initial mask image"
456+ )
447457 max_sh = InputMultiObject (
448458 traits .Int ,
449459 argstr = "-lmax %s" ,
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