diff --git a/fsl/data/image.py b/fsl/data/image.py index 4cd9d02a8c176780542c9d61d528aa40ca33af64..54d74cfa235929c241546e487db7649323eb2960 100644 --- a/fsl/data/image.py +++ b/fsl/data/image.py @@ -815,9 +815,10 @@ class Nifti(notifier.Notifier, meta.Meta): @property + @deprecated.deprecated('3.22.0', '4.0.0', 'Use getAffine instead') def voxToScaledVoxMat(self): - """Returns a transformation matrix which transforms from voxel - coordinates into scaled voxel coordinates, with a left-right flip + """Returns a transformation matrix which transforms from ``voxel`` + coordinates into ``fsl`` coordinates, with a left-right flip if the image appears to be stored in neurological order. See http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#What_is_the\ @@ -828,9 +829,11 @@ class Nifti(notifier.Notifier, meta.Meta): @property + @deprecated.deprecated('3.22.0', '4.0.0', 'Use getAffine instead') def scaledVoxToVoxMat(self): - """Returns a transformation matrix which transforms from scaled voxels - into voxels, the inverse of the :meth:`voxToScaledVoxMat` transform. + """Returns a transformation matrix which transforms from ``fsl`` + coordinates into ``voxel`` coordinates, the inverse of the + :meth:`voxToScaledVoxMat` transform. """ return self.getAffine('fsl', 'voxel') diff --git a/fsl/transform/flirt.py b/fsl/transform/flirt.py index 5acd4b6ff86879897be5a108b1ca1bc2a6b5e29c..a5ac25c022234aa12ab785d3a4d1c4322087b74c 100644 --- a/fsl/transform/flirt.py +++ b/fsl/transform/flirt.py @@ -138,15 +138,15 @@ def sformToFlirtMatrix(srcImage, refImage, srcXform=None): :attr:`.Nifti.voxToWorldMat` """ - srcScaledVoxToVoxMat = srcImage.scaledVoxToVoxMat - srcVoxToWorldMat = srcImage.voxToWorldMat - refWorldToVoxMat = refImage.worldToVoxMat - refVoxToScaledVoxMat = refImage.voxToScaledVoxMat + srcFSLToVoxMat = srcImage.getAffine('fsl', 'voxel') + srcVoxToWorldMat = srcImage.getAffine('voxel', 'world') + refWorldToVoxMat = refImage.getAffine('world', 'voxel') + refVoxToFSLMat = refImage.getAffine('voxel', 'fsl') if srcXform is not None: srcVoxToWorldMat = srcXform - return concat(refVoxToScaledVoxMat, + return concat(refVoxToFSLMat, refWorldToVoxMat, srcVoxToWorldMat, - srcScaledVoxToVoxMat) + srcFSLToVoxMat)