From 69c108ea4e1aabd4dbc17e201523b64b70452387 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 11 Apr 2019 12:39:02 +0100
Subject: [PATCH] RF: VoxelwiseEVMixin has a new getData method which takes
into account compressed voxelwise EVs
---
fsl/data/featdesign.py | 36 +++++++++++++++++++++++++++++++++++-
1 file changed, 35 insertions(+), 1 deletion(-)
diff --git a/fsl/data/featdesign.py b/fsl/data/featdesign.py
index 633b712b4..ce5b41f59 100644
--- a/fsl/data/featdesign.py
+++ b/fsl/data/featdesign.py
@@ -214,7 +214,7 @@ class FEATFSFDesign(object):
'for ev {}'.format(ev.index))
continue
- design[:, ev.index] = ev.image[x, y, z, :]
+ design[:, ev.index] = ev.getData(x, y, z)
return design
@@ -228,6 +228,17 @@ class VoxelwiseEVMixin(object):
``filename`` Path to the image file containing the data for this EV
``image`` Reference to the :class:`.Image` object
============ ======================================================
+
+ Some FSL tools (e.g. `PNM
+ <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PNM>`_) generate *compressed*
+ voxelwise EVs, where there is only one voxel per slice. For example,
+ if the input data has shape ``(x, y, z, t)``, and slices are acquired
+ along the Z plane, voxelwise EV files generated by PNM will have shape
+ ``(1, 1, z, t)``.
+
+ Therefore, using the :meth:`getData` method is preferable to accessing
+ the :meth:`image` directly, as ``getData`` will check for compressed
+ images, and adjust the voxel coordinates accordingly.
"""
def __init__(self, filename):
@@ -272,6 +283,29 @@ class VoxelwiseEVMixin(object):
return self.__image
+ def getData(self, x, y, z):
+ """Returns the data at the specified voxel, taking into account
+ compressed voxelwise EVs.
+ """
+ image = self.image
+
+ if image is None:
+ return None
+
+ dx, dy, dz = image.shape[:3]
+
+ # "Compressed" images have one voxel
+ # per slice, i.e. they have shape
+ # [1, 1, nslices, ntimepoints] (if
+ # Z is the slice plane).
+ if sum((dx == 1, dy == 1, dz == 1)) == 2:
+ if dx == 1: x = 0
+ if dy == 1: y = 0
+ if dz == 1: z = 0
+
+ return image[x, y, z, :]
+
+
class EV(object):
"""Class representing an explanatory variable in a FEAT design matrix.
--
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