From dc5eadb2bccb3a1ea6f29ae7cf202770d9229474 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 21 Sep 2020 18:15:45 +0100
Subject: [PATCH] BF: Adjust fieldToRefMat in case the provided reference image
has different dimensions than the original reference image
---
fsl/transform/fnirt.py | 21 +++++++++++++++++++++
1 file changed, 21 insertions(+)
diff --git a/fsl/transform/fnirt.py b/fsl/transform/fnirt.py
index 4fa4051c8..6357fb9ec 100644
--- a/fsl/transform/fnirt.py
+++ b/fsl/transform/fnirt.py
@@ -225,6 +225,27 @@ def _readFnirtCoefficientField(fname, img, src, ref):
# image voxel coordinates.
fieldToRefMat = affine.scaleOffsetXform(knotSpacing, 0)
+ # But if the provided reference has
+ # different resolution to the
+ # reference that was originally
+ # used to generate the warp field,
+ # we need to adjust the field
+ # accordingly. We assume that the
+ # references are aligned in the FSL
+ # coordinate system, so simply apply
+ # a scaling factor calculated by
+ # dividing the original reference
+ # pixdims by the provided reference
+ # pixdims.
+ refPixdims = np.array([img.header['intent_p1'],
+ img.header['intent_p2'],
+ img.header['intent_p3']])
+
+ if not np.all(np.isclose(ref.pixdim[:3], refPixdims)):
+ fieldToRefMat = affine.concat(
+ affine.scaleOffsetXform(refPixdims / ref.pixdim[:3], 0),
+ fieldToRefMat)
+
return nonlinear.CoefficientField(fname,
src,
ref,
--
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