From 84bd49508148be77449c1288d52972cb0e9cc6f3 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 16 Jul 2019 13:17:01 +0100
Subject: [PATCH] RF: Adjust matrix correctly (again) for >3D images. Adjust
pixdims of higher dimensions
---
fsl/scripts/resample_image.py | 13 +++++++++++++
fsl/utils/image/resample.py | 7 ++++++-
2 files changed, 19 insertions(+), 1 deletion(-)
diff --git a/fsl/scripts/resample_image.py b/fsl/scripts/resample_image.py
index 81b329ce4..b2ef4b9c0 100644
--- a/fsl/scripts/resample_image.py
+++ b/fsl/scripts/resample_image.py
@@ -196,6 +196,19 @@ def main(argv=None):
xform = None
resampled = fslimage.Image(resampled, xform=xform, header=hdr)
+
+ # Adjust the pixdims of the
+ # higher dimensions if they
+ # have been resampled
+ if len(resampled.shape) > 3:
+
+ oldPixdim = args.input.pixdim[3:]
+ oldShape = args.input.shape[ 3:]
+ newShape = resampled .shape[ 3:]
+
+ for i, (p, o, n) in enumerate(zip(oldPixdim, oldShape, newShape), 4):
+ resampled.header['pixdim'][i] = p * o / n
+
resampled.save(args.output)
return 0
diff --git a/fsl/utils/image/resample.py b/fsl/utils/image/resample.py
index 0047444b4..91e79e6c0 100644
--- a/fsl/utils/image/resample.py
+++ b/fsl/utils/image/resample.py
@@ -210,7 +210,12 @@ def resample(image,
# might not return a 4x4 matrix, so we
# make sure it is valid.
if matrix.shape != (4, 4):
- matrix = np.vstack((matrix[:3, :4], [0, 0, 0, 1]))
+ rotmat = matrix[:3, :3]
+ offsets = matrix[:3, -1]
+ matrix = np.eye(4)
+ matrix[:3, :3] = rotmat
+ matrix[:3, -1] = offsets
+
matrix = transform.concat(image.voxToWorldMat, matrix)
return data, matrix
--
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