From 68494421cb08a0f70867a6622534d4b2c2c84394 Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Wed, 15 Aug 2018 13:38:46 +0100
Subject: [PATCH] ref is not compulsary in fnirt if you are using the --config
option jacobian is an output image in convertwarp
---
fsl/wrappers/fnirt.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
diff --git a/fsl/wrappers/fnirt.py b/fsl/wrappers/fnirt.py
index 59ce1b642..f4ca120fc 100644
--- a/fsl/wrappers/fnirt.py
+++ b/fsl/wrappers/fnirt.py
@@ -27,12 +27,12 @@ from . import wrapperutils as wutils
'refout', 'refmask', 'inmask')
@wutils.fileOrArray('aff')
@wutils.fslwrapper
-def fnirt(src, ref, **kwargs):
+def fnirt(src, **kwargs):
"""Wrapper for the ``fnirt`` command."""
- asrt.assertIsNifti(src, ref)
+ asrt.assertIsNifti(src)
- cmd = ['fnirt', '--in={}'.format(src), '--ref={}'.format(ref)]
+ cmd = ['fnirt', '--in={}'.format(src)]
cmd += wutils.applyArgStyle('--=', **kwargs)
return cmd
@@ -75,7 +75,7 @@ def invwarp(warp, ref, out, **kwargs):
'verbose' : wutils.SHOW_IF_TRUE,
}
- asrt.assertIsNifti(warp, ref, out)
+ asrt.assertIsNifti(warp, ref)
cmd = ['invwarp',
'--warp={}'.format(warp),
@@ -87,7 +87,7 @@ def invwarp(warp, ref, out, **kwargs):
return cmd
-@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap')
+@wutils.fileOrImage('out', 'ref', 'warp1', 'warp2', 'shiftmap', 'jacobian')
@wutils.fileOrArray('premat', 'midmat', 'postmat')
@wutils.fslwrapper
def convertwarp(out, ref, **kwargs):
@@ -98,7 +98,6 @@ def convertwarp(out, ref, **kwargs):
'rel' : wutils.SHOW_IF_TRUE,
'absout' : wutils.SHOW_IF_TRUE,
'relout' : wutils.SHOW_IF_TRUE,
- 'jacobian' : wutils.SHOW_IF_TRUE,
'jstats' : wutils.SHOW_IF_TRUE,
'constrainj' : wutils.SHOW_IF_TRUE,
'verbose' : wutils.SHOW_IF_TRUE,
@@ -106,5 +105,4 @@ def convertwarp(out, ref, **kwargs):
cmd = ['convertwarp', '--ref={}'.format(ref), '--out={}'.format(out)]
cmd += wutils.applyArgStyle('--=', valmap=valmap, **kwargs)
-
return cmd
--
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