Merge pull request #635 from poldrack/master

try to determine output dir from fsf file

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 )