From 15ddfed96d2dd833a710388aea5a069247735017 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jul 2019 17:02:43 +0100
Subject: [PATCH] BF: Can't short-cut convertDeformationType, as it causes inf
recursion between DefField.deformationType and detectDeformationType. Also
fix applyDeformation where not using altref
---
fsl/transform/nonlinear.py | 6 +++---
fsl/utils/image/resample.py | 4 +++-
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index 062514700..ab1a9641f 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -582,9 +582,6 @@ def convertDeformationType(field, defType=None):
if field.deformationType == 'absolute': defType = 'relative'
else: defType = 'absolute'
- if field.deformationType == defType:
- return field.data
-
# Regardless of the conversion direction,
# we need the coordinates of every voxel
# in the reference coordinate system.
@@ -743,6 +740,9 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
mode='constant',
cval=-1)[0]
+ else:
+ field = field.data
+
field = field.transpose((3, 0, 1, 2))
return ndinterp.map_coordinates(image.data,
field,
diff --git a/fsl/utils/image/resample.py b/fsl/utils/image/resample.py
index 1aa52b9d2..50dc0c402 100644
--- a/fsl/utils/image/resample.py
+++ b/fsl/utils/image/resample.py
@@ -67,7 +67,9 @@ def resampleToReference(image, reference, matrix=None, **kwargs):
newShape = newShape + oldShape[len(newShape):]
# Align the two images together
- # via their vox-to-world affines.
+ # via their vox-to-world affines,
+ # and the world-to-world affine
+ # if provided
matrix = affine.concat(image.worldToVoxMat,
affine.invert(matrix),
reference.voxToWorldMat)
--
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