Merge pull request #2334 from mvdoc/afni/deconvolve

FIX: some fixes to afni.Deconvolve

Author: effigies

.zenodo.json

@@ -516,6 +516,11 @@
     {
       "name": "Flandin, Guillaume"
     },
+    {
+      "affiliation": "Dartmouth College",
+      "name": "Visconti di Oleggio Castello, Matteo",
+      "orcid": "0000-0001-7931-5272"
+    },
     {
       "affiliation": "CEA",
       "name": "Papadopoulos Orfanos, Dimitri",

nipype/interfaces/afni/model.py

@@ -36,7 +36,7 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         argstr='-input %s',
         copyfile=False,
         sep=" ",
-        position=0)
+        position=1)
     sat = traits.Bool(
         desc='check the dataset time series for initial saturation transients,'
         ' which should normally have been excised before data analysis.',
@@ -57,10 +57,11 @@ class DeconvolveInputSpec(AFNICommandInputSpec):
         '* If the auto-catenation feature isn\'t used, then this option '
         'has no effect, no how, no way.',
         argstr='-noblock')
-    force_TR = traits.Int(
+    force_TR = traits.Float(
         desc='use this value instead of the TR in the \'input\' '
-        'dataset. (It\'s better to fix the input using Refit.)',
-        argstr='-force_TR %d')
+             'dataset. (It\'s better to fix the input using Refit.)',
+        argstr='-force_TR %f',
+        position=0)
     input1D = File(
         desc='filename of single (fMRI) .1D time series where time runs down '
         'the column.',
@@ -294,7 +295,11 @@ def _list_outputs(self):
 
         outputs['reml_script'] = self._gen_fname(
             suffix='.REML_cmd', **_gen_fname_opts)
-        outputs['out_file'] = os.path.abspath(self.inputs.out_file)
+        # remove out_file from outputs if x1d_stop set to True
+        if self.inputs.x1D_stop:
+            del outputs['out_file']
+        else:
+            outputs['out_file'] = os.path.abspath(self.inputs.out_file)
 
         return outputs
 

nipype/interfaces/afni/tests/test_auto_Deconvolve.py

@@ -18,7 +18,10 @@ def test_Deconvolve_inputs():
             nohash=True,
             usedefault=True,
         ),
-        force_TR=dict(argstr='-force_TR %d', ),
+        force_TR=dict(
+            argstr='-force_TR %f',
+            position=0,
+        ),
         fout=dict(argstr='-fout', ),
         global_times=dict(
             argstr='-global_times',
@@ -42,7 +45,7 @@ def test_Deconvolve_inputs():
         in_files=dict(
             argstr='-input %s',
             copyfile=False,
-            position=0,
+            position=1,
             sep=' ',
         ),
         input1D=dict(argstr='-input1D %s', ),

nipype/interfaces/afni/tests/test_extra_Deconvolve.py

@@ -0,0 +1,10 @@
+"""Test afni deconvolve"""
+
+from ..model import Deconvolve
+
+def test_x1dstop():
+    deconv = Deconvolve()
+    deconv.inputs.out_file = 'file.nii'
+    assert 'out_file' in deconv._list_outputs()
+    deconv.inputs.x1D_stop = True
+    assert not 'out_file' in deconv._list_outputs()