From 670811c691853bc39d099211665018b26de7a98d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 16 Jan 2017 16:34:55 +0000
Subject: [PATCH] Image has new voxelsToScaledVoxels method, which returns
scaled voxel xform. Transform module has new flirtMatrixToSform function
which turns a FLIRT matrix into a src -> struc sform transformation.
---
fsl/data/image.py | 23 +++++++++++++++++++++++
fsl/utils/transform.py | 35 +++++++++++++++++++++++++++++++++++
2 files changed, 58 insertions(+)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 0fc1f6ff0..ec8b9fd39 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -422,6 +422,29 @@ class Nifti(notifier.Notifier):
return npla.det(self.__voxToWorldMat) > 0
+ @memoize.Instanceify(memoize.memoize)
+ def voxelsToScaledVoxels(self):
+ """Returns a transformation matrix which transforms from voxel
+ coordinates into scaled voxel 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\
+ _format_of_the_matrix_used_by_FLIRT.2C_and_how_does_it_relate_to\
+ _the_transformation_parameters.3F
+ """
+
+ shape = list(self.shape[ :3])
+ pixdim = list(self.pixdim[:3])
+ voxToPixdimMat = np.diag(pixdim + [1.0])
+
+ if self.isNeurological():
+ x = (shape[0] - 1) * pixdim[0]
+ flip = transform.scaleOffsetXform([-1, 1, 1], [x, 0, 0])
+ voxToPixdimMat = transform.concat(voxToPixdimMat, flip)
+
+ return voxToPixdimMat
+
+
def sameSpace(self, other):
"""Returns ``True`` if the ``other`` image (assumed to be a
:class:`Nifti` instance) has the same dimensions and is in the
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index df82ddc55..f7bd2f21f 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -19,6 +19,7 @@ spaces. The following functions are provided:
rotMatToAxisAngles
axisAnglesToRotMat
axisBounds
+ flirtMatrixToSform
"""
import numpy as np
@@ -378,3 +379,37 @@ def _fillPoints(p, axes):
newp[:, ax] = p[:, i]
return newp
+
+
+def flirtMatrixToSform(flirtMat, srcImage, refImage):
+ """Converts the given ``FLIRT`` transformation matrix into a
+ transformation from the source image voxel coordinate system to
+ the reference image world coordinate system.
+
+ FLIRT transformation matrices transform from the source image scaled voxel
+ coordinate system into the reference image scaled voxel coordinate system
+ (voxels scaled by pixdims, with a left-right flip if the image sform has a
+ positive determinant).
+
+ So to construct a transformation from source image voxel coordinates
+ into reference image world coordinates, we need to combine the following:
+
+ 1. Source voxels -> Source scaled voxels
+ 2. Source scaled voxels -> Reference scaled voxels (the FLIRT matrix)
+ 3. Reference scaled voxels -> Reference voxels
+ 4. Reference voxels -> Reference world (the reference image sform)
+
+ :arg flirtMat: A ``(4, 4)`` transformation matrix
+ :arg srcImage: Source :class:`.Image`
+ :arg refImage: Reference :class:`.Image`
+ """
+
+ srcScaledVoxelMat = srcImage.voxelsToScaledVoxels()
+ refScaledVoxelMat = refImage.voxelsToScaledVoxels()
+ refVoxToWorldMat = refImage.voxToWorldMat
+ refInvScaledVoxelMat = invert(refScaledVoxelMat)
+
+ return concat(refVoxToWorldMat,
+ refInvScaledVoxelMat,
+ flirtMat,
+ srcScaledVoxelMat)
--
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