From 0de7374249c9bb2e4f66c7a26fffd96355bc4bcd Mon Sep 17 00:00:00 2001
From: dPys <dpisner@utexas.edu>
Date: Tue, 24 Mar 2020 15:37:41 -0500
Subject: [PATCH 01/22] [ENH] Add nibabel-based split and merge interfaces per
 https://github.com/nipreps/dmriprep/pull/77

---
 niworkflows/interfaces/nibabel.py | 66 ++++++++++++++++++++++++++++++-
 1 file changed, 65 insertions(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 9364636279b..72784dbdc71 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -7,7 +7,7 @@
 from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec, File,
-    SimpleInterface
+    SimpleInterface, OutputMultiPath, InputMultiPath
 )
 
 IFLOGGER = logging.getLogger('nipype.interface')
@@ -89,3 +89,67 @@ def _run_interface(self, runtime):
         maskimg.to_filename(self._results['out_mask'])
 
         return runtime
+
+class _Save4Dto3DInputSpec(BaseInterfaceInputSpec):
+    in_file = File(exists=True, mandatory=True, desc='input 4d image')
+
+
+class _Save4Dto3DOutputSpec(TraitedSpec):
+    out_files = OutputMultiPath(File(exists=True),
+                                     desc='output list of 3d images')
+
+
+class Save4Dto3D(SimpleInterface):
+    """Split a 4D dataset along the last dimension
+    into multiple 3D volumes."""
+
+    input_spec = _Save4Dto3DInputSpec
+    output_spec = _Save4Dto3DOutputSpec
+
+    def _run_interface(self, runtime):
+        filenii = nb.load(self.inputs.in_file)
+        if len(filenii.shape) != 4:
+            raise RuntimeError('Input image (%s) is not 4D.' % filenii)
+
+        files_3d = nb.four_to_three(filenii)
+        out_files = []
+        for i, file_3d in enumerate(files_3d):
+            out_file = fname_presuffix(in_file, suffix="_tmp_{}".format(i))
+            file_3d.to_filename(out_file)
+            out_files.append(out_file)
+
+        self._results['out_files'] = out_files
+        return runtime
+
+
+class _Save3Dto4DInputSpec(BaseInterfaceInputSpec):
+    in_files = InputMultiPath(File(exists=True, mandatory=True,
+                                   desc='input list of 3d images'))
+
+
+class _Save3Dto4DOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='output list of 3d images')
+
+
+class Save3Dto4D(SimpleInterface):
+    """Merge a list of 3D volumes along the last dimension into a single
+    4D image."""
+
+    input_spec = _Save4Dto3DInputSpec
+    output_spec = _Save4Dto3DOutputSpec
+
+    def _run_interface(self, runtime):
+        nii_list = []
+        for i, f in enumerate(self.inputs.in_files):
+            filenii = nb.load(f)
+            filenii = nb.squeeze_image(filenii)
+            if len(filenii.shape) != 3:
+                raise RuntimeError('Input image (%s) is not 3D.' % f)
+            else:
+                nii_list.append(filenii)
+        img_4d = nb.funcs.concat_images(nii_list)
+        out_file = fname_presuffix(self.inputs.in_files[0], suffix="_merged")
+        img_4d.to_filename(out_file)
+
+        self._results['out_file'] = out_file
+        return runtime

From bfcd29c253539c11976b3beca3d2153c3f48fd8a Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Tue, 24 Mar 2020 16:56:17 -0500
Subject: [PATCH 02/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 72784dbdc71..f0bfc303c99 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -99,7 +99,7 @@ class _Save4Dto3DOutputSpec(TraitedSpec):
                                      desc='output list of 3d images')
 
 
-class Save4Dto3D(SimpleInterface):
+class FourToThree(SimpleInterface):
     """Split a 4D dataset along the last dimension
     into multiple 3D volumes."""
 

From 30ddf03b11be49aa0e47ed68c5986aedfac82083 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Tue, 24 Mar 2020 16:56:25 -0500
Subject: [PATCH 03/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index f0bfc303c99..38bf4eeef1e 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -140,7 +140,7 @@ class Save3Dto4D(SimpleInterface):
 
     def _run_interface(self, runtime):
         nii_list = []
-        for i, f in enumerate(self.inputs.in_files):
+        for f in self.inputs.in_files:
             filenii = nb.load(f)
             filenii = nb.squeeze_image(filenii)
             if len(filenii.shape) != 3:

From 5e3c93c00c497ce99795a59176e6da382ca8ed11 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Tue, 24 Mar 2020 16:56:40 -0500
Subject: [PATCH 04/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 38bf4eeef1e..881a4f5ea31 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -7,7 +7,7 @@
 from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.base import (
     traits, TraitedSpec, BaseInterfaceInputSpec, File,
-    SimpleInterface, OutputMultiPath, InputMultiPath
+    SimpleInterface, OutputMultiObject, InputMultiObject
 )
 
 IFLOGGER = logging.getLogger('nipype.interface')

From 40f6de1a1580d7e44ff33fe5b3cbeb640e42e847 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Tue, 24 Mar 2020 16:56:48 -0500
Subject: [PATCH 05/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/nibabel.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 881a4f5ea31..675b993b7db 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -90,6 +90,7 @@ def _run_interface(self, runtime):
 
         return runtime
 
+
 class _Save4Dto3DInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input 4d image')
 

From f3572e66044c31952cfbf14922a5ab8c5a849902 Mon Sep 17 00:00:00 2001
From: dPys <dpisner@utexas.edu>
Date: Tue, 24 Mar 2020 17:04:04 -0500
Subject: [PATCH 06/22] Chage naming to ConcatImages, fix in/out spec namings

---
 niworkflows/interfaces/nibabel.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 675b993b7db..7710663d9dc 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -91,11 +91,11 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class _Save4Dto3DInputSpec(BaseInterfaceInputSpec):
+class _FourToThreeInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input 4d image')
 
 
-class _Save4Dto3DOutputSpec(TraitedSpec):
+class _FourToThreeOutputSpec(TraitedSpec):
     out_files = OutputMultiPath(File(exists=True),
                                      desc='output list of 3d images')
 
@@ -104,8 +104,8 @@ class FourToThree(SimpleInterface):
     """Split a 4D dataset along the last dimension
     into multiple 3D volumes."""
 
-    input_spec = _Save4Dto3DInputSpec
-    output_spec = _Save4Dto3DOutputSpec
+    input_spec = _FourToThreeInputSpec
+    output_spec = _FourToThreeOutputSpec
 
     def _run_interface(self, runtime):
         filenii = nb.load(self.inputs.in_file)
@@ -123,21 +123,21 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class _Save3Dto4DInputSpec(BaseInterfaceInputSpec):
+class _ConcatImagesInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiPath(File(exists=True, mandatory=True,
                                    desc='input list of 3d images'))
 
 
-class _Save3Dto4DOutputSpec(TraitedSpec):
+class _ConcatImagesOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc='output list of 3d images')
 
 
-class Save3Dto4D(SimpleInterface):
+class ConcatImages(SimpleInterface):
     """Merge a list of 3D volumes along the last dimension into a single
     4D image."""
 
-    input_spec = _Save4Dto3DInputSpec
-    output_spec = _Save4Dto3DOutputSpec
+    input_spec = _ConcatImagesInputSpec
+    output_spec = _ConcatImagesOutputSpec
 
     def _run_interface(self, runtime):
         nii_list = []

From 49ff6bd731534877b59bb31fb5c89cb7d42be05c Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Tue, 31 Mar 2020 15:38:19 -0500
Subject: [PATCH 07/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 7710663d9dc..6e826d775f6 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -96,7 +96,7 @@ class _FourToThreeInputSpec(BaseInterfaceInputSpec):
 
 
 class _FourToThreeOutputSpec(TraitedSpec):
-    out_files = OutputMultiPath(File(exists=True),
+    out_files = OutputMultiObject(File(exists=True),
                                      desc='output list of 3d images')
 
 

From 87f1cb374b7f4bbd001f170390af16ddf654a2a0 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Tue, 31 Mar 2020 15:38:24 -0500
Subject: [PATCH 08/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 6e826d775f6..4baed0ddf83 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -124,7 +124,7 @@ def _run_interface(self, runtime):
 
 
 class _ConcatImagesInputSpec(BaseInterfaceInputSpec):
-    in_files = InputMultiPath(File(exists=True, mandatory=True,
+    in_files = InputMultiObject(File(exists=True, mandatory=True,
                                    desc='input list of 3d images'))
 
 

From b4fcdb71252d59293149b9ad790b6b963fe037d5 Mon Sep 17 00:00:00 2001
From: dPys <dpisner@utexas.edu>
Date: Tue, 31 Mar 2020 16:07:10 -0500
Subject: [PATCH 09/22] rename ConcatImages to MergeSeries, correct typo in
 description of outputs

---
 niworkflows/interfaces/nibabel.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 4baed0ddf83..fe1ff3bfd37 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -102,7 +102,7 @@ class _FourToThreeOutputSpec(TraitedSpec):
 
 class FourToThree(SimpleInterface):
     """Split a 4D dataset along the last dimension
-    into multiple 3D volumes."""
+    into a series of 3D volumes."""
 
     input_spec = _FourToThreeInputSpec
     output_spec = _FourToThreeOutputSpec
@@ -123,21 +123,21 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class _ConcatImagesInputSpec(BaseInterfaceInputSpec):
+class _MergeSeriesInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiObject(File(exists=True, mandatory=True,
                                    desc='input list of 3d images'))
 
 
-class _ConcatImagesOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='output list of 3d images')
+class _MergeSeriesOutputSpec(TraitedSpec):
+    out_file = File(exists=True, desc='output 4d image')
 
 
-class ConcatImages(SimpleInterface):
-    """Merge a list of 3D volumes along the last dimension into a single
+class MergeSeries(SimpleInterface):
+    """Merge a series of 3D volumes along the last dimension into a single
     4D image."""
 
-    input_spec = _ConcatImagesInputSpec
-    output_spec = _ConcatImagesOutputSpec
+    input_spec = _MergeSeriesInputSpec
+    output_spec = _MergeSeriesOutputSpec
 
     def _run_interface(self, runtime):
         nii_list = []

From f51f510a5ea6c7228866715fb171cf4bbb05a494 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Sat, 4 Apr 2020 23:19:43 -0500
Subject: [PATCH 10/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index fe1ff3bfd37..90a6bafa602 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -115,7 +115,7 @@ def _run_interface(self, runtime):
         files_3d = nb.four_to_three(filenii)
         out_files = []
         for i, file_3d in enumerate(files_3d):
-            out_file = fname_presuffix(in_file, suffix="_tmp_{}".format(i))
+            out_file = fname_presuffix(in_file, suffix=f"_idx-{i:03}")
             file_3d.to_filename(out_file)
             out_files.append(out_file)
 

From 9aa065584e3198b56f309d381768e5f91f877870 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Sat, 4 Apr 2020 23:19:53 -0500
Subject: [PATCH 11/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 90a6bafa602..0a076fa4bb3 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -113,7 +113,7 @@ def _run_interface(self, runtime):
             raise RuntimeError('Input image (%s) is not 4D.' % filenii)
 
         files_3d = nb.four_to_three(filenii)
-        out_files = []
+        self._results['out_files'] = []
         for i, file_3d in enumerate(files_3d):
             out_file = fname_presuffix(in_file, suffix=f"_idx-{i:03}")
             file_3d.to_filename(out_file)

From 5a31b01dba9f32d8716cd10f574497be76370c1e Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Sat, 4 Apr 2020 23:20:22 -0500
Subject: [PATCH 12/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 0a076fa4bb3..1c9faa0d722 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -125,7 +125,7 @@ def _run_interface(self, runtime):
 
 class _MergeSeriesInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiObject(File(exists=True, mandatory=True,
-                                   desc='input list of 3d images'))
+                                     desc='input list of 3d images'))
 
 
 class _MergeSeriesOutputSpec(TraitedSpec):

From 53db81aba7f4e6ea31127beee5530eecb23e6fda Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Sat, 4 Apr 2020 23:20:44 -0500
Subject: [PATCH 13/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
---
 niworkflows/interfaces/nibabel.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 1c9faa0d722..a2b22f61719 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -133,8 +133,7 @@ class _MergeSeriesOutputSpec(TraitedSpec):
 
 
 class MergeSeries(SimpleInterface):
-    """Merge a series of 3D volumes along the last dimension into a single
-    4D image."""
+    """Merge a series of 3D volumes along the last dimension into a single 4D image."""
 
     input_spec = _MergeSeriesInputSpec
     output_spec = _MergeSeriesOutputSpec

From 1c27f2048878074a19d28b5a79d21ea5f41206a2 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Sat, 4 Apr 2020 23:22:11 -0500
Subject: [PATCH 14/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
---
 niworkflows/interfaces/nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index a2b22f61719..707c4ffb36c 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -100,7 +100,7 @@ class _FourToThreeOutputSpec(TraitedSpec):
                                      desc='output list of 3d images')
 
 
-class FourToThree(SimpleInterface):
+class SplitSeries(SimpleInterface):
     """Split a 4D dataset along the last dimension
     into a series of 3D volumes."""
 

From 05724d57e1e062422f7e8cfb7b9f788c18cd6d25 Mon Sep 17 00:00:00 2001
From: Derek Pisner <16432683+dPys@users.noreply.github.com>
Date: Sat, 4 Apr 2020 23:30:07 -0500
Subject: [PATCH 15/22] Update niworkflows/interfaces/nibabel.py

Co-Authored-By: Oscar Esteban <code@oscaresteban.es>
---
 niworkflows/interfaces/nibabel.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 707c4ffb36c..721f041ceb3 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -117,9 +117,8 @@ def _run_interface(self, runtime):
         for i, file_3d in enumerate(files_3d):
             out_file = fname_presuffix(in_file, suffix=f"_idx-{i:03}")
             file_3d.to_filename(out_file)
-            out_files.append(out_file)
+            self._results['out_files'].append(out_file)
 
-        self._results['out_files'] = out_files
         return runtime
 
 

From 7263d03c546c721a086f7cdead9f56cdb8cac099 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 8 Apr 2020 12:27:47 -0700
Subject: [PATCH 16/22] Apply suggestions from code review [skip ci]

---
 niworkflows/interfaces/nibabel.py | 32 +++++++++++++++++++++++--------
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 721f041ceb3..fcf9c0c7fd1 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -93,6 +93,7 @@ def _run_interface(self, runtime):
 
 class _FourToThreeInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input 4d image')
+    accept_3D = traits.Bool(False, usedefault=True, desc='do not fail if a 3D volume is passed in')
 
 
 class _FourToThreeOutputSpec(TraitedSpec):
@@ -108,14 +109,25 @@ class SplitSeries(SimpleInterface):
     output_spec = _FourToThreeOutputSpec
 
     def _run_interface(self, runtime):
-        filenii = nb.load(self.inputs.in_file)
-        if len(filenii.shape) != 4:
-            raise RuntimeError('Input image (%s) is not 4D.' % filenii)
+        filenii = nb.squeeze_image(nb.load(self.inputs.in_file))
+        ndim = filenii.dataobj.ndim
+        if ndim != 4:
+            if self.inputs.accept_3D and ndim == 3:
+                out_file = str(
+                    Path(fname_presuffix(self.inputs.in_file, suffix=f"_idx-000")).absolute()
+                )
+                self._results['out_files'] = out_file
+                filenii.to_filename(out_file)
+                return runtime
+            raise RuntimeError(f"Input image image is {ndim}D.")
 
         files_3d = nb.four_to_three(filenii)
         self._results['out_files'] = []
+        in_file = self.inputs.in_file
         for i, file_3d in enumerate(files_3d):
-            out_file = fname_presuffix(in_file, suffix=f"_idx-{i:03}")
+            out_file = str(
+                Path(fname_presuffix(in_file, suffix=f"_idx-{i:03}")).absolute()
+            )
             file_3d.to_filename(out_file)
             self._results['out_files'].append(out_file)
 
@@ -125,6 +137,7 @@ def _run_interface(self, runtime):
 class _MergeSeriesInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiObject(File(exists=True, mandatory=True,
                                      desc='input list of 3d images'))
+    allow_4D = traits.Bool(True, usedefault=True, desc='whether 4D images are allowed to be concatenated')
 
 
 class _MergeSeriesOutputSpec(TraitedSpec):
@@ -142,11 +155,14 @@ def _run_interface(self, runtime):
         for f in self.inputs.in_files:
             filenii = nb.load(f)
             filenii = nb.squeeze_image(filenii)
-            if len(filenii.shape) != 3:
-                raise RuntimeError('Input image (%s) is not 3D.' % f)
-            else:
+            if filenii.dataobj.ndim == 3:
                 nii_list.append(filenii)
-        img_4d = nb.funcs.concat_images(nii_list)
+            elif self.inputs.allow_4D and filenii.dataobj.ndim == 4:
+                nii_list += nb.four_to_three(filenii)
+            else:
+                raise ValueError("Input image has an incorrect number of dimensions"
+                                 f" ({filenii.dataobj.ndim}).")
+        img_4d = nb.concat_images(nii_list)
         out_file = fname_presuffix(self.inputs.in_files[0], suffix="_merged")
         img_4d.to_filename(out_file)
 

From 03ebb6d7064aae298da2e048ce292ab54ab7d3a9 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 8 Apr 2020 12:59:40 -0700
Subject: [PATCH 17/22] fix: added few bugfixes and regression tests

---
 niworkflows/interfaces/nibabel.py            | 25 ++++---
 niworkflows/interfaces/tests/test_nibabel.py | 78 +++++++++++++++++++-
 2 files changed, 92 insertions(+), 11 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index fcf9c0c7fd1..206cae2e3fd 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Nibabel-based interfaces."""
+from pathlib import Path
 import numpy as np
 import nibabel as nb
 from nipype import logging
@@ -98,12 +99,11 @@ class _FourToThreeInputSpec(BaseInterfaceInputSpec):
 
 class _FourToThreeOutputSpec(TraitedSpec):
     out_files = OutputMultiObject(File(exists=True),
-                                     desc='output list of 3d images')
+                                  desc='output list of 3d images')
 
 
 class SplitSeries(SimpleInterface):
-    """Split a 4D dataset along the last dimension
-    into a series of 3D volumes."""
+    """Split a 4D dataset along the last dimension into a series of 3D volumes."""
 
     input_spec = _FourToThreeInputSpec
     output_spec = _FourToThreeOutputSpec
@@ -119,7 +119,8 @@ def _run_interface(self, runtime):
                 self._results['out_files'] = out_file
                 filenii.to_filename(out_file)
                 return runtime
-            raise RuntimeError(f"Input image image is {ndim}D.")
+            raise RuntimeError(
+                f"Input image image is {ndim}D ({'x'.join(['%d' % s for s in filenii.shape])}).")
 
         files_3d = nb.four_to_three(filenii)
         self._results['out_files'] = []
@@ -137,7 +138,8 @@ def _run_interface(self, runtime):
 class _MergeSeriesInputSpec(BaseInterfaceInputSpec):
     in_files = InputMultiObject(File(exists=True, mandatory=True,
                                      desc='input list of 3d images'))
-    allow_4D = traits.Bool(True, usedefault=True, desc='whether 4D images are allowed to be concatenated')
+    allow_4D = traits.Bool(True, usedefault=True,
+                           desc='whether 4D images are allowed to be concatenated')
 
 
 class _MergeSeriesOutputSpec(TraitedSpec):
@@ -153,15 +155,18 @@ class MergeSeries(SimpleInterface):
     def _run_interface(self, runtime):
         nii_list = []
         for f in self.inputs.in_files:
-            filenii = nb.load(f)
-            filenii = nb.squeeze_image(filenii)
-            if filenii.dataobj.ndim == 3:
+            filenii = nb.squeeze_image(nb.load(f))
+            ndim = filenii.dataobj.ndim
+            if ndim == 3:
                 nii_list.append(filenii)
-            elif self.inputs.allow_4D and filenii.dataobj.ndim == 4:
+                continue
+            elif self.inputs.allow_4D and ndim == 4:
                 nii_list += nb.four_to_three(filenii)
+                continue
             else:
                 raise ValueError("Input image has an incorrect number of dimensions"
-                                 f" ({filenii.dataobj.ndim}).")
+                                 f" ({ndim}).")
+
         img_4d = nb.concat_images(nii_list)
         out_file = fname_presuffix(self.inputs.in_files[0], suffix="_merged")
         img_4d.to_filename(out_file)
diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
index abdab406fcf..30aed36cff8 100644
--- a/niworkflows/interfaces/tests/test_nibabel.py
+++ b/niworkflows/interfaces/tests/test_nibabel.py
@@ -4,7 +4,7 @@
 import nibabel as nb
 import pytest
 
-from ..nibabel import Binarize, ApplyMask
+from ..nibabel import Binarize, ApplyMask, SplitSeries, MergeSeries
 
 
 def test_Binarize(tmp_path):
@@ -69,3 +69,79 @@ def test_ApplyMask(tmp_path):
         ApplyMask(in_file=str(in_file), in_mask=str(in_mask), threshold=0.4).run()
     with pytest.raises(ValueError):
         ApplyMask(in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.4).run()
+
+
+def test_SplitSeries(tmp_path):
+    """Test 4-to-3 NIfTI split interface."""
+    os.chdir(str(tmp_path))
+
+    # Test the 4D
+    data = np.ones((20, 20, 20, 15), dtype=float)
+    in_file = tmp_path / 'input4D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    split = SplitSeries(in_file=str(in_file)).run()
+    assert len(split.outputs.out_files) == 15
+
+    # Test the 3D
+    data = np.ones((20, 20, 20), dtype=float)
+    in_file = tmp_path / 'input3D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file)).run()
+
+    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    assert isinstance(split.outputs.out_files, str)
+
+    # Test the 3D
+    data = np.ones((20, 20, 20, 1), dtype=float)
+    in_file = tmp_path / 'input3D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file)).run()
+
+    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    assert isinstance(split.outputs.out_files, str)
+
+    # Test the 5D
+    data = np.ones((20, 20, 20, 2, 2), dtype=float)
+    in_file = tmp_path / 'input5D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file)).run()
+
+    with pytest.raises(RuntimeError):
+        SplitSeries(in_file=str(in_file), accept_3D=True).run()
+
+    # Test splitting ANTs warpfields
+    data = np.ones((20, 20, 20, 1, 3), dtype=float)
+    in_file = tmp_path / 'warpfield.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    split = SplitSeries(in_file=str(in_file)).run()
+    assert len(split.outputs.out_files) == 3
+
+def test_MergeSeries(tmp_path):
+    """Test 3-to-4 NIfTI concatenation interface."""
+    os.chdir(str(tmp_path))
+
+    data = np.ones((20, 20, 20), dtype=float)
+    in_file = tmp_path / 'input3D.nii.gz'
+    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+
+    merge = MergeSeries(in_files=[str(in_file)] * 5).run()
+    assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)
+
+    in_4D = tmp_path / 'input4D.nii.gz'
+    nb.Nifti1Image(
+        np.ones((20, 20, 20, 4), dtype=float), np.eye(4), None
+    ).to_filename(str(in_4D))
+
+    merge = MergeSeries(in_files=[str(in_file)] + [str(in_4D)]).run()
+    assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)
+
+    with pytest.raises(ValueError):
+        MergeSeries(in_files=[str(in_file)] + [str(in_4D)], allow_4D=False).run()

From 9446d47ffecb69d51e65316447bbd7453afab359 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 8 Apr 2020 15:05:10 -0700
Subject: [PATCH 18/22] fix: squeeze image with np.squeeze / change input name
 for consistency

---
 niworkflows/interfaces/nibabel.py            | 11 ++++++++---
 niworkflows/interfaces/tests/test_nibabel.py |  7 ++++---
 2 files changed, 12 insertions(+), 6 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 206cae2e3fd..8da8f428bd3 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -94,7 +94,7 @@ def _run_interface(self, runtime):
 
 class _FourToThreeInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc='input 4d image')
-    accept_3D = traits.Bool(False, usedefault=True, desc='do not fail if a 3D volume is passed in')
+    allow_3D = traits.Bool(False, usedefault=True, desc='do not fail if a 3D volume is passed in')
 
 
 class _FourToThreeOutputSpec(TraitedSpec):
@@ -110,9 +110,12 @@ class SplitSeries(SimpleInterface):
 
     def _run_interface(self, runtime):
         filenii = nb.squeeze_image(nb.load(self.inputs.in_file))
+        filenii = filenii.__class__(
+            np.squeeze(filenii.dataobj), filenii.affine, filenii.header
+        )
         ndim = filenii.dataobj.ndim
         if ndim != 4:
-            if self.inputs.accept_3D and ndim == 3:
+            if self.inputs.allow_3D and ndim == 3:
                 out_file = str(
                     Path(fname_presuffix(self.inputs.in_file, suffix=f"_idx-000")).absolute()
                 )
@@ -120,7 +123,9 @@ def _run_interface(self, runtime):
                 filenii.to_filename(out_file)
                 return runtime
             raise RuntimeError(
-                f"Input image image is {ndim}D ({'x'.join(['%d' % s for s in filenii.shape])}).")
+                f"Input image <{self.inputs.in_file}> is {ndim}D "
+                f"({'x'.join(['%d' % s for s in filenii.shape])})."
+            )
 
         files_3d = nb.four_to_three(filenii)
         self._results['out_files'] = []
diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
index 30aed36cff8..f137ea6192d 100644
--- a/niworkflows/interfaces/tests/test_nibabel.py
+++ b/niworkflows/interfaces/tests/test_nibabel.py
@@ -91,7 +91,7 @@ def test_SplitSeries(tmp_path):
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
 
-    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    split = SplitSeries(in_file=str(in_file), allow_3D=True).run()
     assert isinstance(split.outputs.out_files, str)
 
     # Test the 3D
@@ -102,7 +102,7 @@ def test_SplitSeries(tmp_path):
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
 
-    split = SplitSeries(in_file=str(in_file), accept_3D=True).run()
+    split = SplitSeries(in_file=str(in_file), allow_3D=True).run()
     assert isinstance(split.outputs.out_files, str)
 
     # Test the 5D
@@ -114,7 +114,7 @@ def test_SplitSeries(tmp_path):
         SplitSeries(in_file=str(in_file)).run()
 
     with pytest.raises(RuntimeError):
-        SplitSeries(in_file=str(in_file), accept_3D=True).run()
+        SplitSeries(in_file=str(in_file), allow_3D=True).run()
 
     # Test splitting ANTs warpfields
     data = np.ones((20, 20, 20, 1, 3), dtype=float)
@@ -124,6 +124,7 @@ def test_SplitSeries(tmp_path):
     split = SplitSeries(in_file=str(in_file)).run()
     assert len(split.outputs.out_files) == 3
 
+
 def test_MergeSeries(tmp_path):
     """Test 3-to-4 NIfTI concatenation interface."""
     os.chdir(str(tmp_path))

From 0ae53513f4e5dc9913d63fdb3b53eae2046cf32f Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 8 Apr 2020 15:08:23 -0700
Subject: [PATCH 19/22] sty(black): standardize formatting a bit

---
 niworkflows/interfaces/nibabel.py            | 95 +++++++++++---------
 niworkflows/interfaces/tests/test_nibabel.py | 66 ++++++++------
 2 files changed, 91 insertions(+), 70 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 8da8f428bd3..59bf14c12e0 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -7,22 +7,28 @@
 from nipype import logging
 from nipype.utils.filemanip import fname_presuffix
 from nipype.interfaces.base import (
-    traits, TraitedSpec, BaseInterfaceInputSpec, File,
-    SimpleInterface, OutputMultiObject, InputMultiObject
+    traits,
+    TraitedSpec,
+    BaseInterfaceInputSpec,
+    File,
+    SimpleInterface,
+    OutputMultiObject,
+    InputMultiObject,
 )
 
-IFLOGGER = logging.getLogger('nipype.interface')
+IFLOGGER = logging.getLogger("nipype.interface")
 
 
 class _ApplyMaskInputSpec(BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True, desc='an image')
-    in_mask = File(exists=True, mandatory=True, desc='a mask')
-    threshold = traits.Float(0.5, usedefault=True,
-                             desc='a threshold to the mask, if it is nonbinary')
+    in_file = File(exists=True, mandatory=True, desc="an image")
+    in_mask = File(exists=True, mandatory=True, desc="a mask")
+    threshold = traits.Float(
+        0.5, usedefault=True, desc="a threshold to the mask, if it is nonbinary"
+    )
 
 
 class _ApplyMaskOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='masked file')
+    out_file = File(exists=True, desc="masked file")
 
 
 class ApplyMask(SimpleInterface):
@@ -36,8 +42,9 @@ def _run_interface(self, runtime):
         msknii = nb.load(self.inputs.in_mask)
         msk = msknii.get_fdata() > self.inputs.threshold
 
-        self._results['out_file'] = fname_presuffix(
-            self.inputs.in_file, suffix='_masked', newpath=runtime.cwd)
+        self._results["out_file"] = fname_presuffix(
+            self.inputs.in_file, suffix="_masked", newpath=runtime.cwd
+        )
 
         if img.dataobj.shape[:3] != msk.shape:
             raise ValueError("Image and mask sizes do not match.")
@@ -49,19 +56,18 @@ def _run_interface(self, runtime):
             msk = msk[..., np.newaxis]
 
         masked = img.__class__(img.dataobj * msk, None, img.header)
-        masked.to_filename(self._results['out_file'])
+        masked.to_filename(self._results["out_file"])
         return runtime
 
 
 class _BinarizeInputSpec(BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True, desc='input image')
-    thresh_low = traits.Float(mandatory=True,
-                              desc='non-inclusive lower threshold')
+    in_file = File(exists=True, mandatory=True, desc="input image")
+    thresh_low = traits.Float(mandatory=True, desc="non-inclusive lower threshold")
 
 
 class _BinarizeOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='masked file')
-    out_mask = File(exists=True, desc='output mask')
+    out_file = File(exists=True, desc="masked file")
+    out_mask = File(exists=True, desc="output mask")
 
 
 class Binarize(SimpleInterface):
@@ -73,33 +79,35 @@ class Binarize(SimpleInterface):
     def _run_interface(self, runtime):
         img = nb.load(self.inputs.in_file)
 
-        self._results['out_file'] = fname_presuffix(
-            self.inputs.in_file, suffix='_masked', newpath=runtime.cwd)
-        self._results['out_mask'] = fname_presuffix(
-            self.inputs.in_file, suffix='_mask', newpath=runtime.cwd)
+        self._results["out_file"] = fname_presuffix(
+            self.inputs.in_file, suffix="_masked", newpath=runtime.cwd
+        )
+        self._results["out_mask"] = fname_presuffix(
+            self.inputs.in_file, suffix="_mask", newpath=runtime.cwd
+        )
 
         data = img.get_fdata()
         mask = data > self.inputs.thresh_low
         data[~mask] = 0.0
         masked = img.__class__(data, img.affine, img.header)
-        masked.to_filename(self._results['out_file'])
+        masked.to_filename(self._results["out_file"])
 
-        img.header.set_data_dtype('uint8')
-        maskimg = img.__class__(mask.astype('uint8'), img.affine,
-                                img.header)
-        maskimg.to_filename(self._results['out_mask'])
+        img.header.set_data_dtype("uint8")
+        maskimg = img.__class__(mask.astype("uint8"), img.affine, img.header)
+        maskimg.to_filename(self._results["out_mask"])
 
         return runtime
 
 
 class _FourToThreeInputSpec(BaseInterfaceInputSpec):
-    in_file = File(exists=True, mandatory=True, desc='input 4d image')
-    allow_3D = traits.Bool(False, usedefault=True, desc='do not fail if a 3D volume is passed in')
+    in_file = File(exists=True, mandatory=True, desc="input 4d image")
+    allow_3D = traits.Bool(
+        False, usedefault=True, desc="do not fail if a 3D volume is passed in"
+    )
 
 
 class _FourToThreeOutputSpec(TraitedSpec):
-    out_files = OutputMultiObject(File(exists=True),
-                                  desc='output list of 3d images')
+    out_files = OutputMultiObject(File(exists=True), desc="output list of 3d images")
 
 
 class SplitSeries(SimpleInterface):
@@ -117,9 +125,11 @@ def _run_interface(self, runtime):
         if ndim != 4:
             if self.inputs.allow_3D and ndim == 3:
                 out_file = str(
-                    Path(fname_presuffix(self.inputs.in_file, suffix=f"_idx-000")).absolute()
+                    Path(
+                        fname_presuffix(self.inputs.in_file, suffix=f"_idx-000")
+                    ).absolute()
                 )
-                self._results['out_files'] = out_file
+                self._results["out_files"] = out_file
                 filenii.to_filename(out_file)
                 return runtime
             raise RuntimeError(
@@ -128,27 +138,29 @@ def _run_interface(self, runtime):
             )
 
         files_3d = nb.four_to_three(filenii)
-        self._results['out_files'] = []
+        self._results["out_files"] = []
         in_file = self.inputs.in_file
         for i, file_3d in enumerate(files_3d):
             out_file = str(
                 Path(fname_presuffix(in_file, suffix=f"_idx-{i:03}")).absolute()
             )
             file_3d.to_filename(out_file)
-            self._results['out_files'].append(out_file)
+            self._results["out_files"].append(out_file)
 
         return runtime
 
 
 class _MergeSeriesInputSpec(BaseInterfaceInputSpec):
-    in_files = InputMultiObject(File(exists=True, mandatory=True,
-                                     desc='input list of 3d images'))
-    allow_4D = traits.Bool(True, usedefault=True,
-                           desc='whether 4D images are allowed to be concatenated')
+    in_files = InputMultiObject(
+        File(exists=True, mandatory=True, desc="input list of 3d images")
+    )
+    allow_4D = traits.Bool(
+        True, usedefault=True, desc="whether 4D images are allowed to be concatenated"
+    )
 
 
 class _MergeSeriesOutputSpec(TraitedSpec):
-    out_file = File(exists=True, desc='output 4d image')
+    out_file = File(exists=True, desc="output 4d image")
 
 
 class MergeSeries(SimpleInterface):
@@ -169,12 +181,13 @@ def _run_interface(self, runtime):
                 nii_list += nb.four_to_three(filenii)
                 continue
             else:
-                raise ValueError("Input image has an incorrect number of dimensions"
-                                 f" ({ndim}).")
+                raise ValueError(
+                    "Input image has an incorrect number of dimensions" f" ({ndim})."
+                )
 
         img_4d = nb.concat_images(nii_list)
         out_file = fname_presuffix(self.inputs.in_files[0], suffix="_merged")
         img_4d.to_filename(out_file)
 
-        self._results['out_file'] = out_file
+        self._results["out_file"] = out_file
         return runtime
diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
index f137ea6192d..adc049a0ad3 100644
--- a/niworkflows/interfaces/tests/test_nibabel.py
+++ b/niworkflows/interfaces/tests/test_nibabel.py
@@ -14,10 +14,10 @@ def test_Binarize(tmp_path):
     mask = np.zeros((20, 20, 20), dtype=bool)
     mask[5:15, 5:15, 5:15] = bool
 
-    data = np.zeros_like(mask, dtype='float32')
+    data = np.zeros_like(mask, dtype="float32")
     data[mask] = np.random.gamma(2, size=mask.sum())
 
-    in_file = tmp_path / 'input.nii.gz'
+    in_file = tmp_path / "input.nii.gz"
     nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
 
     binif = Binarize(thresh_low=0.0, in_file=str(in_file)).run()
@@ -36,28 +36,32 @@ def test_ApplyMask(tmp_path):
     mask[8:11, 8:11, 8:11] = 1.0
 
     # Test the 3D
-    in_file = tmp_path / 'input3D.nii.gz'
+    in_file = tmp_path / "input3D.nii.gz"
     nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
 
-    in_mask = tmp_path / 'mask.nii.gz'
+    in_mask = tmp_path / "mask.nii.gz"
     nb.Nifti1Image(mask, np.eye(4), None).to_filename(str(in_mask))
 
     masked1 = ApplyMask(in_file=str(in_file), in_mask=str(in_mask), threshold=0.4).run()
-    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 5**3
+    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 5 ** 3
 
     masked1 = ApplyMask(in_file=str(in_file), in_mask=str(in_mask), threshold=0.6).run()
-    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 3**3
+    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 3 ** 3
 
     data4d = np.stack((data, 2 * data, 3 * data), axis=-1)
     # Test the 4D case
-    in_file4d = tmp_path / 'input4D.nii.gz'
+    in_file4d = tmp_path / "input4D.nii.gz"
     nb.Nifti1Image(data4d, np.eye(4), None).to_filename(str(in_file4d))
 
-    masked1 = ApplyMask(in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.4).run()
-    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 5**3 * 6
+    masked1 = ApplyMask(
+        in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.4
+    ).run()
+    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 5 ** 3 * 6
 
-    masked1 = ApplyMask(in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.6).run()
-    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 3**3 * 6
+    masked1 = ApplyMask(
+        in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.6
+    ).run()
+    assert nb.load(masked1.outputs.out_file).get_fdata().sum() == 3 ** 3 * 6
 
     # Test errors
     nb.Nifti1Image(mask, 2 * np.eye(4), None).to_filename(str(in_mask))
@@ -77,16 +81,17 @@ def test_SplitSeries(tmp_path):
 
     # Test the 4D
     data = np.ones((20, 20, 20, 15), dtype=float)
-    in_file = tmp_path / 'input4D.nii.gz'
+    in_file = tmp_path / "input4D.nii.gz"
     nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
 
     split = SplitSeries(in_file=str(in_file)).run()
     assert len(split.outputs.out_files) == 15
 
     # Test the 3D
-    data = np.ones((20, 20, 20), dtype=float)
-    in_file = tmp_path / 'input3D.nii.gz'
-    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+    in_file = tmp_path / "input3D.nii.gz"
+    nb.Nifti1Image(np.ones((20, 20, 20), dtype=float), np.eye(4), None).to_filename(
+        str(in_file)
+    )
 
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
@@ -95,9 +100,10 @@ def test_SplitSeries(tmp_path):
     assert isinstance(split.outputs.out_files, str)
 
     # Test the 3D
-    data = np.ones((20, 20, 20, 1), dtype=float)
-    in_file = tmp_path / 'input3D.nii.gz'
-    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+    in_file = tmp_path / "input3D.nii.gz"
+    nb.Nifti1Image(np.ones((20, 20, 20, 1), dtype=float), np.eye(4), None).to_filename(
+        str(in_file)
+    )
 
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
@@ -106,9 +112,10 @@ def test_SplitSeries(tmp_path):
     assert isinstance(split.outputs.out_files, str)
 
     # Test the 5D
-    data = np.ones((20, 20, 20, 2, 2), dtype=float)
-    in_file = tmp_path / 'input5D.nii.gz'
-    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+    in_file = tmp_path / "input5D.nii.gz"
+    nb.Nifti1Image(
+        np.ones((20, 20, 20, 2, 2), dtype=float), np.eye(4), None
+    ).to_filename(str(in_file))
 
     with pytest.raises(RuntimeError):
         SplitSeries(in_file=str(in_file)).run()
@@ -118,7 +125,7 @@ def test_SplitSeries(tmp_path):
 
     # Test splitting ANTs warpfields
     data = np.ones((20, 20, 20, 1, 3), dtype=float)
-    in_file = tmp_path / 'warpfield.nii.gz'
+    in_file = tmp_path / "warpfield.nii.gz"
     nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
 
     split = SplitSeries(in_file=str(in_file)).run()
@@ -129,17 +136,18 @@ def test_MergeSeries(tmp_path):
     """Test 3-to-4 NIfTI concatenation interface."""
     os.chdir(str(tmp_path))
 
-    data = np.ones((20, 20, 20), dtype=float)
-    in_file = tmp_path / 'input3D.nii.gz'
-    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
+    in_file = tmp_path / "input3D.nii.gz"
+    nb.Nifti1Image(np.ones((20, 20, 20), dtype=float), np.eye(4), None).to_filename(
+        str(in_file)
+    )
 
     merge = MergeSeries(in_files=[str(in_file)] * 5).run()
     assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)
 
-    in_4D = tmp_path / 'input4D.nii.gz'
-    nb.Nifti1Image(
-        np.ones((20, 20, 20, 4), dtype=float), np.eye(4), None
-    ).to_filename(str(in_4D))
+    in_4D = tmp_path / "input4D.nii.gz"
+    nb.Nifti1Image(np.ones((20, 20, 20, 4), dtype=float), np.eye(4), None).to_filename(
+        str(in_4D)
+    )
 
     merge = MergeSeries(in_files=[str(in_file)] + [str(in_4D)]).run()
     assert nb.load(merge.outputs.out_file).dataobj.shape == (20, 20, 20, 5)

From fc4235159bcbe2ad422cb4c3967bc7aaa51b820a Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Wed, 8 Apr 2020 16:11:23 -0700
Subject: [PATCH 20/22] enh: make i/o specs of SplitSeries more consistent
 [skip ci]

---
 niworkflows/interfaces/nibabel.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index 59bf14c12e0..f7361b7ccf0 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -99,22 +99,22 @@ def _run_interface(self, runtime):
         return runtime
 
 
-class _FourToThreeInputSpec(BaseInterfaceInputSpec):
+class _SplitSeriesInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc="input 4d image")
     allow_3D = traits.Bool(
         False, usedefault=True, desc="do not fail if a 3D volume is passed in"
     )
 
 
-class _FourToThreeOutputSpec(TraitedSpec):
+class _SplitSeriesOutputSpec(TraitedSpec):
     out_files = OutputMultiObject(File(exists=True), desc="output list of 3d images")
 
 
 class SplitSeries(SimpleInterface):
     """Split a 4D dataset along the last dimension into a series of 3D volumes."""
 
-    input_spec = _FourToThreeInputSpec
-    output_spec = _FourToThreeOutputSpec
+    input_spec = _SplitSeriesInputSpec
+    output_spec = _SplitSeriesOutputSpec
 
     def _run_interface(self, runtime):
         filenii = nb.squeeze_image(nb.load(self.inputs.in_file))

From 1d12dd36142e246bd8125acf06fa8840ed3c5910 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 8 Apr 2020 20:51:23 -0700
Subject: [PATCH 21/22] Update niworkflows/interfaces/tests/test_nibabel.py
 [skip ci]

Co-Authored-By: Chris Markiewicz <effigies@gmail.com>
---
 niworkflows/interfaces/tests/test_nibabel.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
index adc049a0ad3..47a63a5df37 100644
--- a/niworkflows/interfaces/tests/test_nibabel.py
+++ b/niworkflows/interfaces/tests/test_nibabel.py
@@ -77,7 +77,7 @@ def test_ApplyMask(tmp_path):
 
 def test_SplitSeries(tmp_path):
     """Test 4-to-3 NIfTI split interface."""
-    os.chdir(str(tmp_path))
+    os.chdir(tmp_path)
 
     # Test the 4D
     data = np.ones((20, 20, 20, 15), dtype=float)

From d65754651fbfb702b0add0bf081ce04574a68955 Mon Sep 17 00:00:00 2001
From: oesteban <code@oscaresteban.es>
Date: Fri, 10 Apr 2020 15:46:21 -0700
Subject: [PATCH 22/22] fix: apply review comments from @effigies, add
 parameterized tests

---
 niworkflows/interfaces/nibabel.py            | 35 +++------
 niworkflows/interfaces/tests/test_nibabel.py | 78 +++++++-------------
 2 files changed, 35 insertions(+), 78 deletions(-)

diff --git a/niworkflows/interfaces/nibabel.py b/niworkflows/interfaces/nibabel.py
index f7361b7ccf0..9c660d1d4c5 100644
--- a/niworkflows/interfaces/nibabel.py
+++ b/niworkflows/interfaces/nibabel.py
@@ -101,9 +101,6 @@ def _run_interface(self, runtime):
 
 class _SplitSeriesInputSpec(BaseInterfaceInputSpec):
     in_file = File(exists=True, mandatory=True, desc="input 4d image")
-    allow_3D = traits.Bool(
-        False, usedefault=True, desc="do not fail if a 3D volume is passed in"
-    )
 
 
 class _SplitSeriesOutputSpec(TraitedSpec):
@@ -117,34 +114,20 @@ class SplitSeries(SimpleInterface):
     output_spec = _SplitSeriesOutputSpec
 
     def _run_interface(self, runtime):
-        filenii = nb.squeeze_image(nb.load(self.inputs.in_file))
-        filenii = filenii.__class__(
-            np.squeeze(filenii.dataobj), filenii.affine, filenii.header
-        )
-        ndim = filenii.dataobj.ndim
-        if ndim != 4:
-            if self.inputs.allow_3D and ndim == 3:
-                out_file = str(
-                    Path(
-                        fname_presuffix(self.inputs.in_file, suffix=f"_idx-000")
-                    ).absolute()
-                )
-                self._results["out_files"] = out_file
-                filenii.to_filename(out_file)
-                return runtime
-            raise RuntimeError(
-                f"Input image <{self.inputs.in_file}> is {ndim}D "
-                f"({'x'.join(['%d' % s for s in filenii.shape])})."
-            )
+        in_file = self.inputs.in_file
+        img = nb.load(in_file)
+        extra_dims = tuple(dim for dim in img.shape[3:] if dim > 1) or (1,)
+        if len(extra_dims) != 1:
+            raise ValueError(f"Invalid shape {'x'.join(str(s) for s in img.shape)}")
+        img = img.__class__(img.dataobj.reshape(img.shape[:3] + extra_dims),
+                            img.affine, img.header)
 
-        files_3d = nb.four_to_three(filenii)
         self._results["out_files"] = []
-        in_file = self.inputs.in_file
-        for i, file_3d in enumerate(files_3d):
+        for i, img_3d in enumerate(nb.four_to_three(img)):
             out_file = str(
                 Path(fname_presuffix(in_file, suffix=f"_idx-{i:03}")).absolute()
             )
-            file_3d.to_filename(out_file)
+            img_3d.to_filename(out_file)
             self._results["out_files"].append(out_file)
 
         return runtime
diff --git a/niworkflows/interfaces/tests/test_nibabel.py b/niworkflows/interfaces/tests/test_nibabel.py
index 47a63a5df37..3ab8c4ffe47 100644
--- a/niworkflows/interfaces/tests/test_nibabel.py
+++ b/niworkflows/interfaces/tests/test_nibabel.py
@@ -75,61 +75,35 @@ def test_ApplyMask(tmp_path):
         ApplyMask(in_file=str(in_file4d), in_mask=str(in_mask), threshold=0.4).run()
 
 
-def test_SplitSeries(tmp_path):
+@pytest.mark.parametrize("shape,exp_n", [
+    ((20, 20, 20, 15), 15),
+    ((20, 20, 20), 1),
+    ((20, 20, 20, 1), 1),
+    ((20, 20, 20, 1, 3), 3),
+    ((20, 20, 20, 3, 1), 3),
+    ((20, 20, 20, 1, 3, 3), -1),
+    ((20, 1, 20, 15), 15),
+    ((20, 1, 20), 1),
+    ((20, 1, 20, 1), 1),
+    ((20, 1, 20, 1, 3), 3),
+    ((20, 1, 20, 3, 1), 3),
+    ((20, 1, 20, 1, 3, 3), -1),
+])
+def test_SplitSeries(tmp_path, shape, exp_n):
     """Test 4-to-3 NIfTI split interface."""
     os.chdir(tmp_path)
 
-    # Test the 4D
-    data = np.ones((20, 20, 20, 15), dtype=float)
-    in_file = tmp_path / "input4D.nii.gz"
-    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
-
-    split = SplitSeries(in_file=str(in_file)).run()
-    assert len(split.outputs.out_files) == 15
-
-    # Test the 3D
-    in_file = tmp_path / "input3D.nii.gz"
-    nb.Nifti1Image(np.ones((20, 20, 20), dtype=float), np.eye(4), None).to_filename(
-        str(in_file)
-    )
-
-    with pytest.raises(RuntimeError):
-        SplitSeries(in_file=str(in_file)).run()
-
-    split = SplitSeries(in_file=str(in_file), allow_3D=True).run()
-    assert isinstance(split.outputs.out_files, str)
-
-    # Test the 3D
-    in_file = tmp_path / "input3D.nii.gz"
-    nb.Nifti1Image(np.ones((20, 20, 20, 1), dtype=float), np.eye(4), None).to_filename(
-        str(in_file)
-    )
-
-    with pytest.raises(RuntimeError):
-        SplitSeries(in_file=str(in_file)).run()
-
-    split = SplitSeries(in_file=str(in_file), allow_3D=True).run()
-    assert isinstance(split.outputs.out_files, str)
-
-    # Test the 5D
-    in_file = tmp_path / "input5D.nii.gz"
-    nb.Nifti1Image(
-        np.ones((20, 20, 20, 2, 2), dtype=float), np.eye(4), None
-    ).to_filename(str(in_file))
-
-    with pytest.raises(RuntimeError):
-        SplitSeries(in_file=str(in_file)).run()
-
-    with pytest.raises(RuntimeError):
-        SplitSeries(in_file=str(in_file), allow_3D=True).run()
-
-    # Test splitting ANTs warpfields
-    data = np.ones((20, 20, 20, 1, 3), dtype=float)
-    in_file = tmp_path / "warpfield.nii.gz"
-    nb.Nifti1Image(data, np.eye(4), None).to_filename(str(in_file))
-
-    split = SplitSeries(in_file=str(in_file)).run()
-    assert len(split.outputs.out_files) == 3
+    in_file = str(tmp_path / "input.nii.gz")
+    nb.Nifti1Image(np.ones(shape, dtype=float), np.eye(4), None).to_filename(in_file)
+
+    _interface = SplitSeries(in_file=in_file)
+    if exp_n > 0:
+        split = _interface.run()
+        n = int(isinstance(split.outputs.out_files, str)) or len(split.outputs.out_files)
+        assert n == exp_n
+    else:
+        with pytest.raises(ValueError):
+            _interface.run()
 
 
 def test_MergeSeries(tmp_path):