From aafd587e405352ecb564bbcc34a4afd23eaaa9be Mon Sep 17 00:00:00 2001
From: Martin Craig <martin.craig@eng.ox.ac.uk>
Date: Tue, 11 Sep 2018 15:01:39 +0100
Subject: [PATCH] Add FSL_ANAT wrapper
---
fsl/wrappers/__init__.py | 1 +
fsl/wrappers/fsl_anat.py | 48 ++++++++++++++++++++++++++++++++++++++++
2 files changed, 49 insertions(+)
create mode 100644 fsl/wrappers/fsl_anat.py
diff --git a/fsl/wrappers/__init__.py b/fsl/wrappers/__init__.py
index 3a0297a3e..52ca6904f 100644
--- a/fsl/wrappers/__init__.py
+++ b/fsl/wrappers/__init__.py
@@ -82,6 +82,7 @@ from .bet import (bet, # noqa
from .eddy import (eddy_cuda, # noqa
topup)
from .fast import (fast,) # noqa
+from .fsl_anat import (fsl_anat,) # noqa
from .flirt import (flirt, # noqa
invxfm,
applyxfm,
diff --git a/fsl/wrappers/fsl_anat.py b/fsl/wrappers/fsl_anat.py
new file mode 100644
index 000000000..b1c2494d4
--- /dev/null
+++ b/fsl/wrappers/fsl_anat.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python
+#
+# fsl_anat.py - Wrapper for the FSL_ANAT command.
+#
+# Author: Martin Craig <martin.craig@eng.ox.ac.uk>
+#
+"""This module provides the :func:`fsl_anat` function, a wrapper for the FSL
+`FSL_ANAT <https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/fsl_anat>`_ command.
+"""
+
+import six
+
+import fsl.utils.assertions as asrt
+from . import wrapperutils as wutils
+
+@wutils.fileOrImage('img', outprefix='out')
+@wutils.fslwrapper
+def fsl_anat(img, out='fsl_anat', **kwargs):
+ """Wrapper for the ``fsl_anat`` command.
+
+ :arg img: Input structural image
+ :arg out: Output directory name
+ """
+ asrt.assertIsNifti(img)
+
+ valmap = {
+ 'weakbias' : wutils.SHOW_IF_TRUE,
+ 'noreorient' : wutils.SHOW_IF_TRUE,
+ 'nocrop' : wutils.SHOW_IF_TRUE,
+ 'nobias' : wutils.SHOW_IF_TRUE,
+ 'noreg' : wutils.SHOW_IF_TRUE,
+ 'nononlinreg' : wutils.SHOW_IF_TRUE,
+ '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]
+ cmd += wutils.applyArgStyle('--=', valmap=valmap, argmap=argmap, singlechar_args=True, **kwargs)
+
+ return cmd
--
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