Merge pull request #1940 from mgxd/doc/constrastmgr

doc: warn contrastmgr deprecation in fsl 5.0.7+

Author: satra

nipype/interfaces/fsl/model.py

@@ -30,7 +30,6 @@
                     BaseInterfaceInputSpec)
 from .base import FSLCommand, FSLCommandInputSpec, Info
 
-
 class Level1DesignInputSpec(BaseInterfaceInputSpec):
     interscan_interval = traits.Float(mandatory=True,
                                       desc='Interscan  interval (in secs)')
@@ -694,18 +693,15 @@ class FILMGLS(FSLCommand):
     """
 
     _cmd = 'film_gls'
-
+    input_spec = FILMGLSInputSpec
+    output_spec = FILMGLSOutputSpec
     if Info.version() and LooseVersion(Info.version()) > LooseVersion('5.0.6'):
         input_spec = FILMGLSInputSpec507
+        output_spec = FILMGLSOutputSpec507
     elif (Info.version() and
             LooseVersion(Info.version()) > LooseVersion('5.0.4')):
         input_spec = FILMGLSInputSpec505
-    else:
-        input_spec = FILMGLSInputSpec
-    if Info.version() and LooseVersion(Info.version()) > LooseVersion('5.0.6'):
-        output_spec = FILMGLSOutputSpec507
-    else:
-        output_spec = FILMGLSOutputSpec
+
 
     def _get_pe_files(self, cwd):
         files = None
@@ -1075,13 +1071,16 @@ class ContrastMgr(FSLCommand):
     """Use FSL contrast_mgr command to evaluate contrasts
 
     In interface mode this file assumes that all the required inputs are in the
-    same location.
+    same location. This has deprecated for FSL versions 5.0.7+ as the necessary
+    corrections file is no longer generated by FILMGLS.
     """
-
+    if Info.version() and LooseVersion(Info.version()) >= LooseVersion("5.0.7"):
+        DeprecationWarning("ContrastMgr is deprecated in FSL 5.0.7+")
     _cmd = 'contrast_mgr'
     input_spec = ContrastMgrInputSpec
     output_spec = ContrastMgrOutputSpec
 
+
     def _run_interface(self, runtime):
         # The returncode is meaningless in ContrastMgr.  So check the output
         # in stderr and if it's set, then update the returncode