diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index 3ede469ebaa70809c73155372de877f20e591e0d..d7cfb940dab078529c3259612ce9fbd5a8b9e6b2 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -2,11 +2,25 @@ This document contains the ``fslpy`` release history in reverse chronological
order.
+3.18.0 (Under development)
+--------------------------
+
+
+Added
+^^^^^
+
+* New wrapper function for the FLIRT `midtrans` command (!443).
+* The :class:`.Image` class now accepts a ``version`` parameter, as an
+ easy way of specifying the NIfTI file format version (!443).
+
+
3.17.0 (Friday 9th February 2024)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+---------------------------------
+
Added
+^^^^^
* New wrapper function for the FLIRT `makerot` command (!441).
* New wrapper functions for the `imcp`, `immv`, `imrm`, `imln`, `imglob` and
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 8157a422ad133b286246f11ed36506849e63dc54..2d69817707a45cf0965d3441e91eb24338dba52b 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1160,6 +1160,7 @@ class Image(Nifti):
dataSource : PathLike = None,
loadMeta : bool = False,
dataMgr : DataManager = None,
+ version : int = None,
**kwargs):
"""Create an ``Image`` object with the given image data or file name.
@@ -1205,6 +1206,12 @@ class Image(Nifti):
:arg dataMgr: Object implementing the :class:`DataManager`
interface, for managing access to the image data.
+
+ :arg version: NIfTI version - either 1 or 2. Only used when creating
+ an image from a numpy array, and when a ``header`` is
+ not provided. Defaults to the value dictated by the
+ ``FSLOUTPUTTYPE`` environment variable.
+
All other arguments are passed through to the ``nibabel.load`` function
(if it is called).
"""
@@ -1219,6 +1226,10 @@ class Image(Nifti):
deprecated.warn('Image(calcRange)', vin='3.9.0', rin='4.0.0',
msg='The calcRange option has no effect')
+ if version not in (None, 1, 2):
+ raise ValueError('Invalid value for version - only NIfTI '
+ 'versions 1 and 2 are supported')
+
nibImage = None
saved = False
@@ -1261,12 +1272,15 @@ class Image(Nifti):
if header is not None: xform = header.get_best_affine()
else: xform = np.identity(4)
- # default to NIFTI1 if FSLOUTPUTTYPE
- # is not set, just to be safe.
+ # NIfTI1 or NIfTI2 - if version was provided,
+ # use that, otherwise use the FSLOUTPUTTYPE
+ # environment variable
if header is None:
outputType = defaultOutputType()
- if 'NIFTI2' in outputType.name: ctr = nib.Nifti2Image
- else: ctr = nib.Nifti1Image
+ if version == 2: ctr = nib.Nifti2Image
+ elif version == 1: ctr = nib.Nifti1Image
+ elif 'NIFTI2' in outputType.name: ctr = nib.Nifti2Image
+ else: ctr = nib.Nifti1Image
# make sure that the data type is correct,
# in case this header was passed in from
diff --git a/fsl/tests/test_image.py b/fsl/tests/test_image.py
index 14a85f59630b092421c874824998e0f00db041ea..3efe06d3b9ef5603fec154fd9f645d3db17c7082 100644
--- a/fsl/tests/test_image.py
+++ b/fsl/tests/test_image.py
@@ -225,6 +225,27 @@ def test_create():
assert np.all(np.isclose(img.pixdim, (2, 3, 4)))
+def test_create_niftiversion():
+
+ data = np.random.random((10, 10, 10))
+
+ with mock.patch.dict(os.environ, FSLOUTPUTTYPE='NIFTI_GZ'):
+ img = fslimage.Image(data)
+ assert img.niftiVersion == 1
+ img = fslimage.Image(data, version=1)
+ assert img.niftiVersion == 1
+ img = fslimage.Image(data, version=2)
+ assert img.niftiVersion == 2
+
+ with mock.patch.dict(os.environ, FSLOUTPUTTYPE='NIFTI2_GZ'):
+ img = fslimage.Image(data)
+ assert img.niftiVersion == 2
+ img = fslimage.Image(data, version=1)
+ assert img.niftiVersion == 1
+ img = fslimage.Image(data, version=2)
+ assert img.niftiVersion == 2
+
+
def test_name_dataSource():
with tempdir():
diff --git a/fsl/tests/test_wrappers/test_wrappers.py b/fsl/tests/test_wrappers/test_wrappers.py
index 090cba02608a45dd654ca9f06491fcfea2260df9..02177828c14db48301ebf08e8c56ef0eb8a32ce7 100755
--- a/fsl/tests/test_wrappers/test_wrappers.py
+++ b/fsl/tests/test_wrappers/test_wrappers.py
@@ -660,3 +660,9 @@ def test_makerot():
assert fw.makerot(90).stdout[0] == f'{exe} -t 90'
assert fw.makerot(90, cov='cov', centre=[10, 10, 10]).stdout[0] == \
f'{exe} -t 90 --cov=cov --centre=10,10,10'
+
+
+def test_midtrans():
+ with testenv('midtrans') as exe:
+ assert fw.midtrans('out', 'xfm1', 'xfm2', 'xfm3').stdout[0] == \
+ f'{exe} -o out xfm1 xfm2 xfm3'
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index fd95d7690aa9e215772c52b0e92817b7441372fe..6cba0e0262a13771824aa24872755672067c1d73 100755
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -129,7 +129,8 @@ from fsl.wrappers.flirt import (flirt,
fixscaleskew,
mcflirt,
standard_space_roi,
- makerot)
+ makerot,
+ midtrans)
from fsl.wrappers.fnirt import (fnirt,
applywarp,
invwarp,
diff --git a/fsl/wrappers/flirt.py b/fsl/wrappers/flirt.py
index 4fa13c6117adec0dca8a6fb3572d97de96cddfdb..67a485a981ffdb3e9ebcda7f1d0f9bfa4def5001 100644
--- a/fsl/wrappers/flirt.py
+++ b/fsl/wrappers/flirt.py
@@ -232,3 +232,21 @@ def makerot(theta, **kwargs):
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
return cmd
+
+
+@wutils.fileOrArray('output', 'transforms', outprefix='separate')
+@wutils.fileOrImage('template')
+@wutils.fslwrapper
+def midtrans(output, *transforms, **kwargs):
+ """Wrapper for the ``midtrans`` command. """
+
+ valmap = {
+ 'verbose' : wutils.SHOW_IF_TRUE,
+ 'debug' : wutils.SHOW_IF_TRUE
+ }
+
+ cmd = ['midtrans']
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
+ cmd += ['-o', output] + list(transforms)
+
+ return cmd