Merge branch 'master' into enh/restingwf

* master:
  removed save_warped flag from FUGUE call since it doesn't seem to exist in the FUGUE interface
  try to determine output dir from fsf file, to deal with cases where the output dir is not in the cwd

Author: satra

nipype/interfaces/fsl/model.py

@@ -384,16 +384,26 @@ class FEAT(FSLCommand):
     def _list_outputs(self):
         outputs = self._outputs().get()
         is_ica = False
+        outputs['feat_dir']=None
         with open(self.inputs.fsf_file, 'rt') as fp:
             text = fp.read()
             if "set fmri(inmelodic) 1" in text:
                 is_ica = True
-
-        if is_ica:
-            outputs['feat_dir'] = glob(os.path.join(os.getcwd(), '*ica'))[0]
-        else:
-            outputs['feat_dir'] = glob(os.path.join(os.getcwd(), '*feat'))[0]
-
+            for line in text.split('\n'):
+                if line.find("set fmri(outputdir)")>-1:
+                    try:
+                        outputdir_spec=line.split('"')[-2]
+                        if os.path.exists(outputdir_spec):
+                           outputs['feat_dir']=outputdir_spec
+
+                    except:
+                        pass
+        if not outputs['feat_dir']:
+            if is_ica:
+                outputs['feat_dir'] = glob(os.path.join(os.getcwd(), '*ica'))[0]
+            else:
+                outputs['feat_dir'] = glob(os.path.join(os.getcwd(), '*feat'))[0]
+        print 'Outputs from FEATmodel:',outputs
         return outputs
 
 

nipype/workflows/dmri/fsl/dti.py

@@ -521,8 +521,7 @@ def create_susceptibility_correct_pipeline(name="susceptibility_correct", fieldm
 
         # fugue -i %s -w %s --loadshift=%s --mask=%s % ( mag_name, magfw_name,
         # vsmmag_name, mask_name ), log ) # Forward Map
-        vsm_fwd = pe.Node(interface=fsl.FUGUE(
-            save_warped=True), name="vsm_fwd")
+        vsm_fwd = pe.Node(interface=fsl.FUGUE(), name="vsm_fwd")
         vsm_reg = pe.Node(interface=fsl.FLIRT(bins=256, cost='corratio', dof=6, interp='spline',  searchr_x=[
                           -10, 10], searchr_y=[-10, 10], searchr_z=[-10, 10]), name="vsm_registration")
         # 'flirt -in %s -ref %s -out %s -init %s -applyxfm' % ( vsmmag_name, ref_epi, vsmmag_name, magfw_mat_out )