diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index 41d8ab6fdd..cd1da560da 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -240,6 +240,50 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec): desc="input image / directory", ) out_file = File(argstr="%s", mandatory=True, position=-1, desc="output image") + t2_image = File( + exists=True, + argstr="-t2 %s", + desc="Provide a T2-weighted image in addition to the default T1-weighted image. (Only for 'fsl' algorithm)", + ) + mask_file = File( + exists=True, + argstr="-mask %s", + desc="Provide a brain mask image. (Only for 'fsl' algorithm)", + ) + premasked = traits.Bool( + argstr="-premasked", + desc="Assume that the input image is already brain-masked. (Only for 'fsl' algorithm)", + ) + nocrop = traits.Bool( + argstr="-nocrop", + desc="Do not crop the image to the region of interest.", + ) + sgm_amyg_hipp = traits.Bool( + argstr="-sgm_amyg_hipp", + desc="Include the amygdala and hippocampus in the subcortical grey matter segment.", + ) + template = File( + exists=True, + argstr="-template %s", + desc="Provide an image that will form the template for the generated 5TT image. (Only for 'hsvs' algorithm)", + ) + hippocampi = traits.Enum( + "subfields", + "first", + "aseg", + argstr="-hippocampi %s", + desc="Choose the method used to segment the hippocampi. (Only for 'freesurfer' algorithm)", + usedefault=False, + ) + white_stem = traits.Bool( + argstr="-white_stem", + desc="Classify the brainstem as white matter. (Only for 'hsvs' algorithm)", + ) + lut_file = File( + exists=True, + argstr="-lut %s", + desc="Manually provide path to the lookup table on which the input parcellation image is based. (Only for 'freesurfer' algorithm)", + ) class Generate5ttOutputSpec(TraitedSpec):