From 25865a2a50266aff3593cc0355ef246bf04aea01 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 28 Jan 2020 16:34:55 +0000
Subject: [PATCH] ENH: New voxToSurfMat, for generating a freesurfer affine for
any image.
---
fsl/data/mghimage.py | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/fsl/data/mghimage.py b/fsl/data/mghimage.py
index be29b5cad..bdac26012 100644
--- a/fsl/data/mghimage.py
+++ b/fsl/data/mghimage.py
@@ -128,3 +128,30 @@ class MGHImage(fslimage.Image):
coordinates into the surface coordinate system for this image.
"""
return self.__worldToSurfMat
+
+
+def voxToSurfMat(img):
+ """Generate an affine which can transform the voxel coordinates of
+ the given image into a corresponding Freesurfer surface coordinate
+ system (known as "Torig", or "vox2ras-tkr").
+
+ See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
+
+ :arg img: An :class:`.Image` object.
+
+ :return: A ``(4, 4)`` matrix encoding an affine transformation from the
+ image voxel coordinate system to the corresponding Freesurfer
+ surface coordinate system.
+ """
+
+ zooms = np.array(img.pixdim[:3])
+ dims = img.shape[ :3] * zooms / 2
+
+ xform = np.zeros((4, 4), dtype=np.float32)
+ xform[ 0, 0] = -zooms[0]
+ xform[ 1, 2] = zooms[2]
+ xform[ 2, 1] = -zooms[1]
+ xform[ 3, 3] = 1
+ xform[:3, 3] = [dims[0], -dims[2], dims[1]]
+
+ return xform
--
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