Merge pull request #440 from akeshavan/fix/randomise

Fix/randomise: outputs

Author: satra

nipype/interfaces/freesurfer/model.py

@@ -679,7 +679,7 @@ class Label2VolInputSpec(FSTraitedSpec):
                                desc='list of label files')
     annot_file = File(exists=True, argstr='--annot %s',
                      xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'),
-                     requires=('subjectid', 'hemi'),
+                     requires=('subject_id', 'hemi'),
                      mandatory=True,
                      copyfile=False,
                      desc='surface annotation file')
@@ -712,7 +712,7 @@ class Label2VolInputSpec(FSTraitedSpec):
     proj = traits.Tuple(traits.Enum('abs', 'frac'), traits.Float,
                         traits.Float, traits.Float,
                         argstr='--proj %s %f %f %f',
-                        requries=('subjectid', 'hemi'),
+                        requries=('subject_id', 'hemi'),
                         desc='project along surface normal')
     subject_id = traits.Str(argstr='--subject %s',
                            desc='subject id')
@@ -755,9 +755,9 @@ def _list_outputs(self):
         outfile = self.inputs.vol_label_file
         if not isdefined(outfile):
             for key in ['label_file', 'annot_file', 'seg_file']:
-                if isdefined(self.inputs.label_file):
+                if isdefined(getattr(self.inputs,key)):
                     _, src = os.path.split(getattr(self.inputs, key))
-            if isdefined(self.inputs.aparcaaseg):
+            if isdefined(self.inputs.aparc_aseg):
                 src = 'aparc+aseg.mgz'
             outfile = fname_presuffix(src, suffix='_vol.nii.gz',
                                       newpath=os.getcwd(),

nipype/interfaces/freesurfer/tests/test_model.py

@@ -132,7 +132,7 @@ def test_glmfit():
 def test_label2vol():
     input_map = dict(annot_file = dict(copyfile=False, mandatory=True,
                                        xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'),
-                                       requires=('subjectid', 'hemi'), argstr='--annot %s',),
+                                       requires=('subject_id', 'hemi'), argstr='--annot %s',),
                      aparc_aseg = dict(xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'),
                                        argstr='--aparc+aseg', mandatory=True,),
                      args = dict(argstr='%s',),

nipype/interfaces/fsl/model.py

@@ -1487,11 +1487,9 @@ class Randomise(FSLCommand):
 
     def _list_outputs(self):
         outputs = self.output_spec().get()
-        outputs['tstat_files'] = glob(os.path.join(
-                os.getcwd(),
+        outputs['tstat_files'] = glob(self._gen_fname(\
                 '%s_tstat*.nii' % self.inputs.base_name))
-        outputs['fstat_files'] = glob(os.path.join(
-                os.getcwd(),
+        outputs['fstat_files'] = glob(self._gen_fname(\
                 '%s_fstat*.nii' % self.inputs.base_name))
         prefix = False
         if self.inputs.tfce or self.inputs.tfce2D:
@@ -1503,18 +1501,13 @@ def _list_outputs(self):
         elif self.inputs.cm_thresh or self.inputs.f_cm_thresh:
             prefix = 'clusterm'
         if prefix:
-            outputs['t_p_files'] = glob(os.path.join(
-                os.getcwd(),
-                '%s_%s_p_tstat*.nii' % (self.inputs.base_name, prefix)))
-            outputs['t_corrected_p_files'] = glob(os.path.join(
-                os.getcwd(),
+            outputs['t_p_files'] = glob(self._gen_fname(\
+                     '%s_%s_p_tstat*' % (self.inputs.base_name, prefix)))
+            outputs['t_corrected_p_files'] = glob(self._gen_fname(\
                 '%s_%s_corrp_tstat*.nii' % (self.inputs.base_name, prefix)))
 
-            outputs['f_p_files'] = glob(os.path.join(
-                os.getcwd(),
+            outputs['f_p_files'] = glob(self._gen_fname(\
                 '%s_%s_p_fstat*.nii' % (self.inputs.base_name, prefix)))
-            outputs['f_corrected_p_files'] = glob(os.path.join(
-                os.getcwd(),
+            outputs['f_corrected_p_files'] = glob(self._gen_fname(\
                 '%s_%s_corrp_fstat*.nii' % (self.inputs.base_name, prefix)))
-
         return outputs