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Michiel Cottaar
fslpy
Commits
6ef44e19
Commit
6ef44e19
authored
8 years ago
by
Paul McCarthy
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Fix to Nifti1 handling of images with unknown qform/sform codes.
parent
19a30365
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fsl/data/image.py
+32
-8
32 additions, 8 deletions
fsl/data/image.py
with
32 additions
and
8 deletions
fsl/data/image.py
+
32
−
8
View file @
6ef44e19
...
...
@@ -95,6 +95,23 @@ class Nifti1(object):
if
len
(
shape
)
<
3
or
len
(
shape
)
>
4
:
raise
RuntimeError
(
'
Only 3D or 4D images are supported
'
)
voxToWorldMat
=
self
.
__determineTransform
(
header
)
worldToVoxMat
=
transform
.
invert
(
voxToWorldMat
)
self
.
header
=
header
self
.
shape
=
shape
self
.
__origShape
=
origShape
self
.
pixdim
=
pixdim
self
.
voxToWorldMat
=
voxToWorldMat
self
.
worldToVoxMat
=
worldToVoxMat
def
__determineTransform
(
self
,
header
):
"""
Called by :meth:`__init__`. Figures out the voxel-to-world
coordinate transformation matrix that is associated with this
``Nifti1`` instance.
"""
# We have to treat FSL/FNIRT images
# specially, as FNIRT clobbers the
# sform section of the NIFTI header
...
...
@@ -106,19 +123,26 @@ class Nifti1(object):
log
.
debug
(
'
FNIRT output image detected - using qform matrix
'
)
voxToWorldMat
=
np
.
array
(
header
.
get_qform
())
# If the qform or sform codes are unknown,
# then we can't assume that the transform
# matrices are valid. So we fall back to a
# pixdim scaling matrix.
#
# n.b. For images like this, nibabel returns
# a scaling matrix where the centre voxel
# corresponds to world location (0, 0, 0).
# This goes against the NIFTI1 spec - it
# should just be a straight scaling matrix.
elif
header
[
'
qform_code
'
]
==
0
or
header
[
'
sform_code
'
]
==
0
:
pixdims
=
header
.
get_zooms
()
voxToWorldMat
=
transform
.
scaleOffsetXform
(
pixdims
,
0
)
# Otherwise we let nibabel decide
# which transform to use.
else
:
voxToWorldMat
=
np
.
array
(
header
.
get_best_affine
())
worldToVoxMat
=
transform
.
invert
(
voxToWorldMat
)
self
.
header
=
header
self
.
shape
=
shape
self
.
__origShape
=
origShape
self
.
pixdim
=
pixdim
self
.
voxToWorldMat
=
voxToWorldMat
self
.
worldToVoxMat
=
worldToVoxMat
return
voxToWorldMat
def
__determineShape
(
self
,
header
):
...
...
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