From 6a841565c84b56a4ab80ca95acb26b0183c07b5d Mon Sep 17 00:00:00 2001
From: Alexandre Routier <alexandre.routier@gmail.com>
Date: Fri, 6 Aug 2021 22:50:02 +0200
Subject: [PATCH 1/3] Add -mask flag to DWI2Tensor

---
 nipype/interfaces/mrtrix/preprocess.py | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/nipype/interfaces/mrtrix/preprocess.py b/nipype/interfaces/mrtrix/preprocess.py
index 48f4bde719..e9effe5943 100644
--- a/nipype/interfaces/mrtrix/preprocess.py
+++ b/nipype/interfaces/mrtrix/preprocess.py
@@ -217,6 +217,13 @@ class DWI2TensorInputSpec(CommandLineInputSpec):
             "specified when computing the tensor."
         ),
     )
+    mask = File(
+        exists=True,
+        argstr="-mask %s",
+        desc=(
+            "Only perform computation within the specified binary brain mask image."
+        ),
+    )
     quiet = traits.Bool(
         argstr="-quiet",
         position=1,

From 53dd0a4cc0fb57b4c3b26651ada40186d6d006dc Mon Sep 17 00:00:00 2001
From: Alexandre Routier <alexandre.routier@gmail.com>
Date: Fri, 6 Aug 2021 22:50:39 +0200
Subject: [PATCH 2/3] Add -linear flag to MRTransform

---
 nipype/interfaces/mrtrix/preprocess.py | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/nipype/interfaces/mrtrix/preprocess.py b/nipype/interfaces/mrtrix/preprocess.py
index e9effe5943..495f3af703 100644
--- a/nipype/interfaces/mrtrix/preprocess.py
+++ b/nipype/interfaces/mrtrix/preprocess.py
@@ -872,6 +872,17 @@ class MRTransformInputSpec(CommandLineInputSpec):
         position=1,
         desc="Invert the specified transform before using it",
     )
+    linear_transform = File(
+        exists=True,
+        argstr="-linear %s",
+        position=1,
+        desc=(
+            "Specify a linear transform to apply, in the form of a 3x4 or 4x4 ascii file. "
+            "Note the standard reverse convention is used, "
+            "where the transform maps points in the template image to the moving image. "
+            "Note that the reverse convention is still assumed even if no -template image is supplied."
+        ),
+    )
     replace_transform = traits.Bool(
         argstr="-replace",
         position=1,

From a1d56ab17b49994752e7a32d01f65b08bd90e45b Mon Sep 17 00:00:00 2001
From: Alexandre Routier <alexandre.routier@gmail.com>
Date: Sun, 8 Aug 2021 22:32:45 +0200
Subject: [PATCH 3/3] Add tests from make check-before-commit

---
 nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py  | 4 ++++
 nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py | 5 +++++
 2 files changed, 9 insertions(+)

diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py
index 25bae449e3..72a2820cc1 100644
--- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py
+++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py
@@ -35,6 +35,10 @@ def test_DWI2Tensor_inputs():
             mandatory=True,
             position=-2,
         ),
+        mask=dict(
+            argstr="-mask %s",
+            extensions=None,
+        ),
         out_filename=dict(
             argstr="%s",
             extensions=None,
diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py
index c1e91da1c1..f619525575 100644
--- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py
+++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py
@@ -28,6 +28,11 @@ def test_MRTransform_inputs():
             argstr="-inverse",
             position=1,
         ),
+        linear_transform=dict(
+            argstr="-linear %s",
+            extensions=None,
+            position=1,
+        ),
         out_filename=dict(
             argstr="%s",
             extensions=None,