Add outputspec and reml_script.

Author: tsalo

nipype/interfaces/afni/model.py

@@ -87,10 +87,17 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         desc='Build a mask automatically from input data (will be slow for '
              'long time series datasets)',
         argstr='-automask')
+    STATmask = File(
+        desc='Build a mask from input file, and use this mask for the purpose '
+             'of reporting truncation-to float issues AND for computing the '
+             'FDR curves. The actual results ARE not masked with this option '
+             '(only with \'mask\' or \'automask\' options).',
+        argstr='-STATmask %s',
+        exists=True)
     censor = File(
-        desc='Filename of censor .1D time series. This is a file of 1s and 0s, '
-             'indicating which time points are to be included (1) and which '
-             'are to be excluded (0).',
+        desc='Filename of censor .1D time series. This is a file of 1s and '
+             '0s, indicating which time points are to be included (1) and '
+             'which are to be excluded (0).',
         argstr='-censor %s',
         exists=True)
     polort = traits.Int(
@@ -181,8 +188,9 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
 
 
 class DeconvolveOutputSpec(AFNICommandOutputSpec):
-    out_file = File(desc='output statistics file',
-                    exists=True)
+    out_file = File(desc='output statistics file')
+    reml_script = File(desc='Autogenerated script for 3dREML')
+    x1D = File(desc='save out X matrix')
 
 
 class Deconvolve(AFNICommand):
@@ -202,16 +210,16 @@ class Deconvolve(AFNICommand):
     >>> stim_times = [(1, 'timeseries.txt', 'SPMG1(4)'), (2, 'timeseries.txt', 'SPMG2(4)')]
     >>> deconvolve.inputs.stim_times = stim_times
     >>> deconvolve.inputs.stim_label = [(1, 'Houses'), (2, 'Apartments')]
-    >>> deconvolve.inputs.gltsym = [('SYM: +Houses -Apartments')]
-    >>> deconvolve.inputs.glt_label = [(1, 'Houses-Apartments')]
+    >>> deconvolve.inputs.gltsym = [('+Houses -Apartments')]
+    >>> deconvolve.inputs.glt_label = [(1, 'Houses_Apartments')]
     >>> deconvolve.cmdline  # doctest: +ALLOW_UNICODE
     '3dDeconvolve -num_stimts 2 -num_glt 1 -glt_label 1 Houses_Apartments -gltsym SYM: +Houses -Apartments -input functional.nii functional2.nii -bucket output.nii -stim_label 1 Houses -stim_label 2 Apartments -stim_times 1 timeseries.txt SPMG1(4) -stim_times 2 timeseries.txt SPMG2(4) -x1D output.1D'
     >>> res = deconvolve.run()  # doctest: +SKIP
     """
 
     _cmd = '3dDeconvolve'
     input_spec = DeconvolveInputSpec
-    output_spec = AFNICommandOutputSpec
+    output_spec = DeconvolveOutputSpec
 
     def _parse_inputs(self, skip=None):
         if skip is None:
@@ -230,5 +238,10 @@ def _list_outputs(self):
             else:
                 outputs['x1D'] = self.inputs.x1D
 
+        _gen_fname_opts = {}
+        _gen_fname_opts['basename'] = self.inputs.out_file
+        _gen_fname_opts['cwd'] = os.getcwd()
+
+        outputs['reml_script'] = self._gen_fname(suffix='.REML_cmd', **_gen_fname_opts)
         outputs['out_file'] = self.inputs.out_file
         return outputs