From 62b151c71d1f04e5488aee2350c225b854a4e4dd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 24 Jan 2017 17:07:47 +0000
Subject: [PATCH] New function to transform module to generate a FLIRT matrix.
Bugfix in melodic labels - failing when trying to load a label file with no
noise components.
---
fsl/data/melodiclabels.py | 6 ++++--
fsl/utils/transform.py | 30 ++++++++++++++++++++++++++++++
2 files changed, 34 insertions(+), 2 deletions(-)
diff --git a/fsl/data/melodiclabels.py b/fsl/data/melodiclabels.py
index 1b09858a8..add891dc5 100644
--- a/fsl/data/melodiclabels.py
+++ b/fsl/data/melodiclabels.py
@@ -423,8 +423,10 @@ def loadLabelFile(filename, includeLabel=None, excludeLabel=None):
else:
melDir = lines[0]
- noisyComps = map(int, lines[-1].strip(' []').split(','))
-
+ noisyComps = lines[-1].strip(' []').split(',')
+ noisyComps = [c for c in noisyComps if c != '']
+ noisyComps = [int(c) for c in noisyComps]
+
# The melodic directory path should
# either be an absolute path, or
# be specified relative to the location
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index f7bd2f21f..36af95c95 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -20,6 +20,7 @@ spaces. The following functions are provided:
axisAnglesToRotMat
axisBounds
flirtMatrixToSform
+ sformToFlirtMatrix
"""
import numpy as np
@@ -413,3 +414,32 @@ def flirtMatrixToSform(flirtMat, srcImage, refImage):
refInvScaledVoxelMat,
flirtMat,
srcScaledVoxelMat)
+
+
+def sformToFlirtMatrix(srcImage, refImage, srcXform=None):
+ """Under the assumption that the given ``srcImage`` and ``refImage``
+ share a common world coordinate system (defined by their
+ :attr:`voxToWorldMat` attributes), this function will calculate and
+ return a transformation matrix from the ``srcImage`` scaled voxel
+ coordinate system to the ``refImage`` scaled voxel coordinate system,
+ that can be saved to disk and used with FLIRT, to resample the source
+ image to the reference image.
+
+ :arg srcImage: Source :class:`.Image`
+ :arg refImage: Reference :class:`.Image`
+ :arg srcXform: Optionally used in place of the ``scrImage``
+ :attr:`.voxToWorldMat`
+ """
+
+ srcScaledVoxelsToVoxelsMat = invert(srcImage.voxelsToScaledVoxels())
+ srcVoxToWorldMat = srcImage.voxToWorldMat
+ refWorldToVoxMat = invert(refImage.voxToWorldMat)
+ refVoxelsToScaledVoxelsMat = refImage.voxelsToScaledVoxels()
+
+ if srcXform is not None:
+ srcVoxToWorldMat = srcXform
+
+ return concat(refVoxelsToScaledVoxelsMat,
+ refWorldToVoxMat,
+ srcVoxToWorldMat,
+ srcScaledVoxelsToVoxelsMat)
--
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