Merge pull request #3658 from GalKepler/5ttgen

[ENH] Added available inputs for MRTrix3's 5ttgen

Author: effigies

nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py

@@ -28,6 +28,9 @@ def test_Generate5tt_inputs():
             argstr="-fslgrad %s %s",
             xor=["grad_file"],
         ),
+        hippocampi=dict(
+            argstr="-hippocampi %s",
+        ),
         in_bval=dict(
             extensions=None,
         ),
@@ -40,6 +43,17 @@ def test_Generate5tt_inputs():
             mandatory=True,
             position=-2,
         ),
+        lut_file=dict(
+            argstr="-lut %s",
+            extensions=None,
+        ),
+        mask_file=dict(
+            argstr="-mask %s",
+            extensions=None,
+        ),
+        nocrop=dict(
+            argstr="-nocrop",
+        ),
         nthreads=dict(
             argstr="-nthreads %d",
             nohash=True,
@@ -57,6 +71,23 @@ def test_Generate5tt_inputs():
             mandatory=True,
             position=-1,
         ),
+        premasked=dict(
+            argstr="-premasked",
+        ),
+        sgm_amyg_hipp=dict(
+            argstr="-sgm_amyg_hipp",
+        ),
+        t2_image=dict(
+            argstr="-t2 %s",
+            extensions=None,
+        ),
+        template=dict(
+            argstr="-template %s",
+            extensions=None,
+        ),
+        white_stem=dict(
+            argstr="-white_stem",
+        ),
     )
     inputs = Generate5tt.input_spec()
 

nipype/interfaces/mrtrix3/utils.py

@@ -241,6 +241,49 @@ 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)",
+    )
+    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):