From 9f3310d42aa4ddf3b723e98d78b4bd152be84a9e Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Tue, 17 Jul 2018 09:58:25 +0100
Subject: [PATCH] Special case to handle 'centre' argument for BET since this
needs to be passed as a sequence of CL arguments, not a single value
---
fsl/wrappers/bet.py | 9 +++++++++
1 file changed, 9 insertions(+)
diff --git a/fsl/wrappers/bet.py b/fsl/wrappers/bet.py
index 09282f117..e20ee3fb1 100644
--- a/fsl/wrappers/bet.py
+++ b/fsl/wrappers/bet.py
@@ -35,6 +35,7 @@ def bet(input, output, **kwargs):
'robust' : 'R',
'fracintensity' : 'f',
'seg' : 'n',
+ 'centre' : 'c',
}
valmap = {
@@ -55,6 +56,14 @@ def bet(input, output, **kwargs):
}
cmd = ['bet', input, output]
+
+ # The 'centre' argument requires three co-ordinates and can't be passed
+ # as a single value, so needs to be handled separately. Assume it is
+ # passed as a Python sequence
+ centre = kwargs.pop("c", None)
+ if centre is not None:
+ cmd += ['c', ] + list(centre)
+
cmd += wutils.applyArgStyle('-', argmap=argmap, valmap=valmap, **kwargs)
return cmd
--
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