From d5137c30c8bdfc5e28ce0519e6a2581514d777f5 Mon Sep 17 00:00:00 2001
From: Eric Condamine <37933899+servoz@users.noreply.github.com>
Date: Tue, 11 Dec 2018 11:00:20 +0100
Subject: [PATCH] Wrong last tuple in the channel_info parameter

In SPM, the spm.spatial.preproc.channel.write parameter (SPM's Save Bias Corrected parameter) takes [Save Bias Field = 0 or 1, Save Bias Corrected = 0 or 1]. In nypipe the initialisation of the outputs bias_field_images and bias_corrected_images are done with the inverse order. This commit fix this inconsistency.
---
 nipype/interfaces/spm/preprocess.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py
index d23887c890..2188824022 100644
--- a/nipype/interfaces/spm/preprocess.py
+++ b/nipype/interfaces/spm/preprocess.py
@@ -1487,7 +1487,7 @@ class NewSegmentInputSpec(SPMCommandInputSpec):
         desc="""A tuple with the following fields:
             - bias reguralisation (0-10)
             - FWHM of Gaussian smoothness of bias
-            - which maps to save (Corrected, Field) - a tuple of two boolean values""",
+            - which maps to save (Field, Corrected) - a tuple of two boolean values""",
         field='channel')
     tissues = traits.List(
         traits.Tuple(
@@ -1681,11 +1681,11 @@ def _list_outputs(self):
 
             if isdefined(self.inputs.channel_info):
                 if self.inputs.channel_info[2][0]:
-                    outputs['bias_corrected_images'].append(
-                        os.path.join(pth, "m%s.nii" % (base)))
-                if self.inputs.channel_info[2][1]:
                     outputs['bias_field_images'].append(
                         os.path.join(pth, "BiasField_%s.nii" % (base)))
+                if self.inputs.channel_info[2][1]:
+                    outputs['bias_corrected_images'].append(
+                        os.path.join(pth, "m%s.nii" % (base)))
         return outputs