Merge remote-tracking branch 'nipy/master' into mriscombine

Author: tsalo

nipype/interfaces/dcm2nii.py

@@ -309,7 +309,10 @@ def _parse_stdout(self, stdout):
                 else:
                     pass
                 if out_file:
-                    files.append(out_file + ".nii.gz")
+                    if self.inputs.compress == 'n':
+                        files.append(out_file + ".nii")
+                    else:
+                        files.append(out_file + ".nii.gz")
                     if self.inputs.bids_format:
                         bids.append(out_file + ".json")
                     continue

nipype/interfaces/fsl/model.py

@@ -30,24 +30,24 @@
                     BaseInterfaceInputSpec)
 from .base import FSLCommand, FSLCommandInputSpec, Info
 
-
 class Level1DesignInputSpec(BaseInterfaceInputSpec):
     interscan_interval = traits.Float(mandatory=True,
                                       desc='Interscan  interval (in secs)')
     session_info = traits.Any(mandatory=True,
                               desc=('Session specific information generated '
                                     'by ``modelgen.SpecifyModel``'))
     bases = traits.Either(
-        traits.Dict(traits.Enum(
-            'dgamma'), traits.Dict(traits.Enum('derivs'), traits.Bool)),
+        traits.Dict(traits.Enum('dgamma'), traits.Dict(
+            traits.Enum('derivs'), traits.Bool)),
         traits.Dict(traits.Enum('gamma'), traits.Dict(
-                    traits.Enum('derivs', 'gammasigma', 'gammadelay'))),
-        traits.Dict(traits.Enum('custom'), traits.Dict(traits.Dict(traits.Enum('bfcustompath'), traits.Str))),
+            traits.Enum('derivs', 'gammasigma', 'gammadelay'))),
+        traits.Dict(traits.Enum('custom'), traits.Dict(
+            traits.Enum('bfcustompath'), traits.Str)),
         traits.Dict(traits.Enum('none'), traits.Dict()),
         traits.Dict(traits.Enum('none'), traits.Enum(None)),
         mandatory=True,
         desc=("name of basis function and options e.g., "
-              "{'dgamma': {'derivs': True}}"))
+              "{'dgamma': {'derivs': True}}"),)
     orthogonalization = traits.Dict(traits.Int, traits.Dict(traits.Int,
         traits.Either(traits.Bool,traits.Int)),
         desc=("which regressors to make orthogonal e.g., "
@@ -211,7 +211,7 @@ def _create_ev_files(
                     try:
                         ev_parameters['temporalderiv'] = int(bool(ev_parameters.pop('derivs')))
                     except KeyError:
-                        pass
+                        ev_parameters['temporalderiv'] = False
                     if ev_parameters['temporalderiv']:
                         evname.append(name + 'TD')
                         num_evs[1] += 1
@@ -395,7 +395,7 @@ def _list_outputs(self):
                         try:
                             ev_parameters['temporalderiv'] = int(bool(ev_parameters.pop('derivs')))
                         except KeyError:
-                            pass
+                            ev_parameters['temporalderiv'] = False
                         if ev_parameters['temporalderiv']:
                             evname.append(name + 'TD')
                     outputs['ev_files'][runno].append(
@@ -694,18 +694,15 @@ 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 +1072,16 @@ 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

nipype/interfaces/fsl/preprocess.py

@@ -649,7 +649,7 @@ class MCFLIRTOutputSpec(TraitedSpec):
     out_file = File(exists=True, desc="motion-corrected timeseries")
     variance_img = File(exists=True, desc="variance image")
     std_img = File(exists=True, desc="standard deviation image")
-    mean_img = File(exists=True, desc="mean timeseries image")
+    mean_img = File(exists=True, desc="mean timeseries image (if mean_vol=True)")
     par_file = File(exists=True, desc="text-file with motion parameters")
     mat_file = OutputMultiPath(File(
         exists=True), desc="transformation matrices")

nipype/interfaces/script_templates/feat_ev_custom.tcl

@@ -37,4 +37,4 @@ set fmri(custom$ev_num) "$cond_file"
 set fmri(default_bfcustom) "${fsldir}/etc/default_flobs.flobs/hrfbasisfns.txt"
 set fmri(basisorth$ev_num) $basisorth
 set fmri(basisfnum$ev_num) $basisfnum
-set fmri(bfcustom) "$bfcustompath"
+set fmri(bfcustom$ev_num) "$bfcustompath"

nipype/pipeline/engine/workflows.py

@@ -425,6 +425,9 @@ def write_graph(self, dotfilename='graph.dot', graph2use='hierarchical',
                 base_dir = os.getcwd()
         base_dir = make_output_dir(base_dir)
         if graph2use in ['hierarchical', 'colored']:
+            if self.name[:1].isdigit(): # these graphs break if int
+                raise ValueError('{} graph failed, workflow name cannot begin '
+                                 'with a number'.format(graph2use))
             dotfilename = op.join(base_dir, dotfilename)
             self.write_hierarchical_dotfile(dotfilename=dotfilename,
                                             colored=graph2use == "colored",