From 7dd64d786e020c5198d45a057c146fac95ccb57a Mon Sep 17 00:00:00 2001
From: GalKepler <galkepler@gmail.com>
Date: Sat, 20 Jul 2024 18:11:39 +0300
Subject: [PATCH 1/3] added available inputs for 5ttgen

---
 nipype/interfaces/mrtrix3/utils.py | 44 ++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index 7e25288d1e..b38e3f4593 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -241,6 +241,50 @@ 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):

From c46f684654fd84c2c4b2f7d2adcdb000b2be610d Mon Sep 17 00:00:00 2001
From: GalKepler <galkepler@gmail.com>
Date: Sat, 20 Jul 2024 18:18:56 +0300
Subject: [PATCH 2/3] tests automatically updated

---
 .../mrtrix3/tests/test_auto_Generate5tt.py    | 32 +++++++++++++++++++
 1 file changed, 32 insertions(+)

diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
index 949fa26280..abc5b0c2eb 100644
--- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
+++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
@@ -28,6 +28,10 @@ def test_Generate5tt_inputs():
             argstr="-fslgrad %s %s",
             xor=["grad_file"],
         ),
+        hippocampi=dict(
+            argstr="-hippocampi %s",
+            usedefault=False,
+        ),
         in_bval=dict(
             extensions=None,
         ),
@@ -40,6 +44,17 @@ 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 +72,23 @@ 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()
 

From 386dd145e8767c25c780fb8466a9ca3846751498 Mon Sep 17 00:00:00 2001
From: GalKepler <galkepler@gmail.com>
Date: Sat, 20 Jul 2024 18:24:34 +0300
Subject: [PATCH 3/3] changed usedefault kwarg for hippocampi input

---
 nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py | 1 -
 nipype/interfaces/mrtrix3/utils.py                       | 1 -
 2 files changed, 2 deletions(-)

diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
index abc5b0c2eb..d8f6e53364 100644
--- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
+++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py
@@ -30,7 +30,6 @@ def test_Generate5tt_inputs():
         ),
         hippocampi=dict(
             argstr="-hippocampi %s",
-            usedefault=False,
         ),
         in_bval=dict(
             extensions=None,
diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py
index b38e3f4593..8a69232ecd 100644
--- a/nipype/interfaces/mrtrix3/utils.py
+++ b/nipype/interfaces/mrtrix3/utils.py
@@ -274,7 +274,6 @@ class Generate5ttInputSpec(MRTrix3BaseInputSpec):
         "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",