save outputs to cwd

Author: Shoshana Berleant

nipype/algorithms/confounds.py

@@ -423,7 +423,7 @@ def _run_interface(self, runtime):
         mask = mask.astype(int).T
 
         # save mask
-        mask_file = 'mask.nii'
+        mask_file = os.path.abspath('mask.nii')
         nb.nifti1.save(nb.Nifti1Image(mask, np.eye(4)), mask_file)
         IFLOG.debug('tCompcor computed and saved mask of shape {} to mask_file {}'
                    .format(mask.shape, mask_file))

nipype/interfaces/nilearn.py

@@ -13,6 +13,7 @@
 '''
 from __future__ import (print_function, division, unicode_literals,
                         absolute_import)
+import os
 
 import numpy as np
 import nibabel as nb
@@ -85,7 +86,7 @@ def _run_interface(self, runtime):
         output = np.vstack((self.inputs.class_labels, region_signals.astype(str)))
 
         # save output
-        np.savetxt(self.inputs.out_file, output, fmt=b'%s', delimiter='\t')
+        np.savetxt(os.path.abspath(self.inputs.out_file), output, fmt=b'%s', delimiter='\t')
         return runtime
 
     def _process_inputs(self):