From 588f2bf8e35f8ce9d4a2524ffac67ef75695ca02 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 23 Jul 2019 15:19:08 +0100
Subject: [PATCH] RF: applyDeformation supports input image with different FOV
to original source image
---
fsl/transform/nonlinear.py | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index 82776bfe6..55fd48ec8 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -745,6 +745,8 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
# truncation at the field boundaries,
# but there's nothing we can do about
# that.
+ src = field.src
+
if not field.sameSpace(ref):
field = resample.resampleToReference(field,
ref,
@@ -755,6 +757,21 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
else:
field = field.data
+ # If the input image is in a
+ # different space to the field
+ # source space, we need to
+ # adjust the resampling matrix.
+ # We assume world-world alignment
+ # between the original source
+ # and the image to be resampled
+ if not image.sameSpace(src):
+ post = affine.concat(image.getAffine('world', 'voxel'),
+ src .getAffine('voxel', 'world'))
+ shape = field.shape
+ field = field.reshape((-1, 3))
+ field = affine.transform(field, post)
+ field = field.reshape(shape)
+
field = field.transpose((3, 0, 1, 2))
return ndinterp.map_coordinates(image.data,
field,
--
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