@@ -241,6 +241,50 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
241241 desc = "input image / directory" ,
242242 )
243243 out_file = File (argstr = "%s" , mandatory = True , position = - 1 , desc = "output image" )
244+ t2_image = File (
245+ exists = True ,
246+ argstr = "-t2 %s" ,
247+ desc = "Provide a T2-weighted image in addition to the default T1-weighted image. (Only for 'fsl' algorithm)" ,
248+ )
249+ mask_file = File (
250+ exists = True ,
251+ argstr = "-mask %s" ,
252+ desc = "Provide a brain mask image. (Only for 'fsl' algorithm)" ,
253+ )
254+ premasked = traits .Bool (
255+ argstr = "-premasked" ,
256+ desc = "Assume that the input image is already brain-masked. (Only for 'fsl' algorithm)" ,
257+ )
258+ nocrop = traits .Bool (
259+ argstr = "-nocrop" ,
260+ desc = "Do not crop the image to the region of interest." ,
261+ )
262+ sgm_amyg_hipp = traits .Bool (
263+ argstr = "-sgm_amyg_hipp" ,
264+ desc = "Include the amygdala and hippocampus in the subcortical grey matter segment." ,
265+ )
266+ template = File (
267+ exists = True ,
268+ argstr = "-template %s" ,
269+ desc = "Provide an image that will form the template for the generated 5TT image. (Only for 'hsvs' algorithm)" ,
270+ )
271+ hippocampi = traits .Enum (
272+ "subfields" ,
273+ "first" ,
274+ "aseg" ,
275+ argstr = "-hippocampi %s" ,
276+ desc = "Choose the method used to segment the hippocampi. (Only for 'freesurfer' algorithm)" ,
277+ usedefault = False ,
278+ )
279+ white_stem = traits .Bool (
280+ argstr = "-white_stem" ,
281+ desc = "Classify the brainstem as white matter. (Only for 'hsvs' algorithm)" ,
282+ )
283+ lut_file = File (
284+ exists = True ,
285+ argstr = "-lut %s" ,
286+ desc = "Manually provide path to the lookup table on which the input parcellation image is based. (Only for 'freesurfer' algorithm)" ,
287+ )
244288
245289
246290class Generate5ttOutputSpec (TraitedSpec ):
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