From 2f1e421b0b3cc9465891aef7645d2875ea5dc302 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 3 Jun 2019 12:18:37 +0100
Subject: [PATCH] BF: Only FNIRT coefficient fields clobber NIFTI headers -
displacement fields are fine. Generating a slightly less incorrect (but still
incorrect) v2w affine for the former. Bug in test script
---
fsl/data/image.py | 23 +++++++++++++++----
.../{ => test_scripts}/test_fsl_convert_x5.py | 2 +-
2 files changed, 20 insertions(+), 5 deletions(-)
rename tests/{ => test_scripts}/test_fsl_convert_x5.py (95%)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 637e745af..b2f07648e 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -312,12 +312,27 @@ class Nifti(notifier.Notifier, meta.Meta):
qform = header.get('qform_code', -1)
sform = header.get('sform_code', -1)
- if intent in (constants.FSL_FNIRT_DISPLACEMENT_FIELD,
- constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
+ # FNIRT non-linear coefficient files
+ # clobber the sform/qform/intent
+ # and pixdims of the nifti header,
+ # so we can't correctly place it in
+ # the world coordinate system. See
+ # $FSLDIR/src/fnirt/fnirt_file_writer.cpp
+ # and fsl.transform.nonlinear for more
+ # details.
+ if intent in (constants.FSL_CUBIC_SPLINE_COEFFICIENTS,
constants.FSL_DCT_COEFFICIENTS,
constants.FSL_QUADRATIC_SPLINE_COEFFICIENTS):
- log.debug('FNIRT output image detected - using qform matrix')
- voxToWorldMat = np.array(header.get_qform())
+
+ log.debug('FNIRT coefficient field detected - generating affine')
+
+ knotpix = header.get_zooms()[:3]
+ refpix = (header.get('intent_p1', 1),
+ header.get('intent_p2', 1),
+ header.get('intent_p3', 1))
+ voxToWorldMat = transform.concat(
+ transform.scaleOffsetXform(refpix, 0),
+ transform.scaleOffsetXform(knotpix, 0))
# If the qform or sform codes are unknown,
# then we can't assume that the transform
diff --git a/tests/test_fsl_convert_x5.py b/tests/test_scripts/test_fsl_convert_x5.py
similarity index 95%
rename from tests/test_fsl_convert_x5.py
rename to tests/test_scripts/test_fsl_convert_x5.py
index 0dab1ec52..e14b3c259 100644
--- a/tests/test_fsl_convert_x5.py
+++ b/tests/test_scripts/test_fsl_convert_x5.py
@@ -43,7 +43,7 @@ def test_convert_flirt():
ref.getAffine('fsl', 'world'),
xform,
src.getAffine('world', 'fsl'))
- gotxform, gotsrc, gotref = transform.readFlirtX5('src2ref.x5')
+ gotxform, gotsrc, gotref = transform.readLinearX5('src2ref.x5')
assert np.all(np.isclose(gotxform, expxform))
assert src.sameSpace(gotsrc)
assert ref.sameSpace(gotref)
--
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