From 25145d182dca91b77f2cf9a12381462f3106c8c0 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 25 May 2016 12:43:19 +0100
Subject: [PATCH] FNIRT-specific hack - using qform matrix for FNIRT output
images.
---
fsl/data/image.py | 22 +++++++++++++++++++---
1 file changed, 19 insertions(+), 3 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 8ca0d1ed2..fbebad533 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -150,9 +150,25 @@ class Nifti1(object):
shape, pixdim = self.__determineShape(self.nibImage)
- self.shape = shape
- self.pixdim = pixdim
- self.voxToWorldMat = np.array(self.nibImage.get_affine())
+ self.shape = shape
+ self.pixdim = pixdim
+
+ # We have to treat FSL/FNIRT images
+ # specially, as FNIRT clobbers the
+ # sform section of the NIFTI header
+ # to store other data. The hard coded
+ # numbers here are the intent codes
+ # output by FNIRT.
+ intent = self.nibImage.get_header().get('intent_code', -1)
+ if intent in (2006, 2007, 2008, 2009):
+ log.debug('FNIRT output image detected - using qform matrix')
+ self.voxToWorldMat = self.nibImage.get_qform()
+
+ # Otherwise we let nibabel decide
+ # which transform to use.
+ else:
+ self.voxToWorldMat = np.array(self.nibImage.get_affine())
+
self.worldToVoxMat = transform.invert(self.voxToWorldMat)
if loadData:
--
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