From 801b6b7c9c70cbef84738d397abaddfc62811c78 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 3 May 2018 11:30:26 +0100
Subject: [PATCH] BF: Fixed invalid assumptions: - not all atlases have a
2mm version - label atlas value does not correspond to its index in the
AtlasDescription.labels list.
---
fsl/scripts/atlasq.py | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/fsl/scripts/atlasq.py b/fsl/scripts/atlasq.py
index bd2459490..502965767 100644
--- a/fsl/scripts/atlasq.py
+++ b/fsl/scripts/atlasq.py
@@ -275,17 +275,27 @@ def ohi(namespace):
dumpatlases()
return
+ # atlasquery always uses 2mm atlas
+ # versions when a 2mm is available
+ reses = [p[0] for p in atlasDesc.pixdims]
+
+ if 2 in reses: res = 2
+ else: res = max(reses)
+
# Mask query.
if namespace.ohiMask is not None:
- # atlasquery always uses 2mm atlas versions
mask = fslimage.Image(namespace.ohiMask)
- labels, props = maskQuery(atlasDesc, [mask], resolution=2)
+ labels, props = maskQuery(atlasDesc, [mask], resolution=res)
labels = labels[0]
props = props[ 0]
for lbl, prop in zip(labels, props):
- lbl = atlasDesc.labels[int(lbl)].name
+
+ if atlasDesc.atlasType == 'probabilistic':
+ lbl = atlasDesc.labels[int(lbl)].name
+ elif atlasDesc.atlasType == 'label':
+ lbl = atlasDesc.find(value=int(lbl)).name
print('{}:{:0.4f}'.format(lbl, prop))
# Coordinate query
@@ -295,7 +305,7 @@ def ohi(namespace):
labels, props = coordQuery(atlasDesc,
[coord],
False,
- resolution=2)
+ resolution=res)
labels = labels[0]
props = props[ 0]
--
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