From 158d705759e36c178a251da5121ee9393a2eb9b0 Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Fri, 21 Sep 2018 15:30:30 +0100
Subject: [PATCH] Single char arguments require special handling here Also fix
betfparam and strongbias arguments
---
fsl/wrappers/fsl_anat.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/fsl/wrappers/fsl_anat.py b/fsl/wrappers/fsl_anat.py
index b1c2494d4..a1ea260c1 100644
--- a/fsl/wrappers/fsl_anat.py
+++ b/fsl/wrappers/fsl_anat.py
@@ -24,6 +24,7 @@ def fsl_anat(img, out='fsl_anat', **kwargs):
asrt.assertIsNifti(img)
valmap = {
+ 'strongbias' : wutils.SHOW_IF_TRUE,
'weakbias' : wutils.SHOW_IF_TRUE,
'noreorient' : wutils.SHOW_IF_TRUE,
'nocrop' : wutils.SHOW_IF_TRUE,
@@ -33,16 +34,18 @@ def fsl_anat(img, out='fsl_anat', **kwargs):
'noseg' : wutils.SHOW_IF_TRUE,
'nosubcortseg' : wutils.SHOW_IF_TRUE,
'nosearch' : wutils.SHOW_IF_TRUE,
- 'betfparam' : wutils.SHOW_IF_TRUE,
'nocleanup' : wutils.SHOW_IF_TRUE,
}
argmap = {
- 'bias_smoothing' : 's',
- 'img_type' : 't',
}
- cmd = ['fsl_anat', '-i', img, '-o', out]
+ img_type = kwargs.pop("img_type", "T1")
+ cmd = ['fsl_anat', '-i', img, '-o', out, '-t', img_type]
+ smoothing = kwargs.pop("bias_smoothing", None)
+ if smoothing is not None:
+ cmd += ['-s', str(smoothing)]
+
cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
return cmd
--
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