Merge pull request nipy#2 from tsalo/afni-deconvolve

Afni deconvolve

Author: rmarkello

nipype/interfaces/afni/model.py

@@ -158,10 +158,6 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         requires=['glt_sym'])
 
 
-class DeconvolveOutputSpec(TraitedSpec):
-    pass
-
-
 class Deconvolve(AFNICommand):
     """Performs OLS regression given a 4D neuroimage file and stimulus timings
 
@@ -179,19 +175,23 @@ class Deconvolve(AFNICommand):
     >>> stim_times = [(1, 'stims1.txt', 'SPMG1(4)'), (2, 'stims2.txt', 'SPMG2(4)')]
     >>> deconvolve.inputs.stim_times = stim_times
     >>> deconvolve.cmdline  # doctest: +ALLOW_UNICODE
-    '3dDeconvolve -input functional.nii -bucket output.nii -x1D output.1D -stim_times 1 stims1.txt SPMG1(4) 2 stims2.txt SPMG2(4)'
+    '3dDeconvolve -input functional.nii -bucket output.nii -x1D output -stim_times 1 stims1.txt SPMG1(4) 2 stims2.txt SPMG2(4)'
     >>> res = deconvolve.run()  # doctest: +SKIP
     """
 
     _cmd = '3dDeconvolve'
     input_spec = DeconvolveInputSpec
-    output_spec = DeconvolveOutputSpec
+    output_spec = AFNICommandOutputSpec
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
         if isdefined(self.inputs.x1D):
             if not self.inputs.x1D.endswith('.xmat.1D'):
-                outputs['x1D'] = outputs['x1D'] + '.xmat.1D'
+                outputs['x1D'] = self.inputs.x1D + '.xmat.1D'
+            else:
+                outputs['x1D'] = self.inputs.x1D
+
+        outputs['bucket'] = self.inputs.bucket
         return outputs
 
     def _format_arg(self, name, trait_spec, value):
@@ -206,5 +206,8 @@ def _format_arg(self, name, trait_spec, value):
                 arg += trait_spec.argstr % value
             arg = arg.rstrip()
             return arg
+
+        if name == 'stim_times':
+            self.inputs.num_stimts = len(value)
         elif name == 'glt_sym':
             self.inputs.num_glt = len(value)