From d635bdae927ea5f850bffb72d91fcc955e7e44a3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 7 Nov 2017 14:03:22 +0000
Subject: [PATCH] If an xform and header are provided, make sure they are
consistent.
---
fsl/data/image.py | 15 ++++++++++++++-
1 file changed, 14 insertions(+), 1 deletion(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 2cc88b840..a5791d458 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -753,7 +753,9 @@ class Image(Nifti):
coordinates. If not provided, and a ``header`` is
provided, the transformation in the header is used.
If neither a ``xform`` nor a ``header`` are provided,
- an identity matrix is used.
+ an identity matrix is used. If both a ``xform`` and a
+ ``header`` are provided, the ``xform`` is used in
+ preference to the header transformation.
:arg loadData: If ``True`` (the default) the image data is loaded
in to memory. Otherwise, only the image header
@@ -799,6 +801,17 @@ class Image(Nifti):
if header is not None:
header = header.copy()
+ # if a header and xform are provided,
+ # make sure the xform gets used. Does
+ # not apply to ANALYZE images,
+ if header is not None and \
+ xform is not None and \
+ isinstance(header, nib.nifti1.Nifti1Header):
+ sform = int(header.get_sform(True)[1])
+ qform = int(header.get_qform(True)[1])
+ header.set_sform(xform, code=sform)
+ header.set_qform(xform, code=qform)
+
# The image parameter may be the name of an image file
if isinstance(image, six.string_types):
--
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