added slice_encoding_direction input to TShift

Author: fliem

nipype/interfaces/afni/preprocess.py

@@ -2618,6 +2618,10 @@ class TShiftInputSpec(AFNICommandInputSpec):
         desc='time offsets from the volume acquisition onset for each slice',
         argstr='-tpattern @%s',
         xor=['tpattern'])
+    slice_encoding_direction = traits.Enum(
+        ('k', 'k-'),
+        desc='Direction in which slice_timing is specified (default: k). If negative,'
+             'slice_timing is defined in reverse order -- see BIDS specification for details.',)
     rlt = traits.Bool(
         desc='Before shifting, remove the mean and linear trend',
         argstr='-rlt')
@@ -2723,9 +2727,17 @@ def _format_arg(self, name, trait_spec, value):
         return super(TShift, self)._format_arg(name, trait_spec, value)
 
     def _write_slice_timing(self):
+        slice_timing = self.inputs.slice_timing.copy()
+        if not self.inputs.slice_encoding_direction:
+            slice_encoding_direction = "k"
+        else:
+            slice_encoding_direction = self.inputs.slice_encoding_direction
+        if slice_encoding_direction.endswith("-"):
+            slice_timing.reverse()
+            
         fname = 'slice_timing.1D'
         with open(fname, 'w') as fobj:
-            fobj.write('\t'.join(map(str, self.inputs.slice_timing)))
+            fobj.write('\t'.join(map(str, slice_timing)))
         return fname
 
     def _list_outputs(self):