Merge pull request #2753 from fliem/slice_direction

[ENH] Add slice_encoding_direction input to TShift

Author: effigies

.zenodo.json

@@ -320,7 +320,9 @@
  "name": "Ghayoor, Ali"
  },
  {
- "name": "Liem, Franz"
+ "affiliation": "University of Zurich",
+ "name": "Liem, Franz",
+ "orcid": "0000-0003-0646-4810"
  },
  {
  "name": "Millman, Jarrod"

nipype/interfaces/afni/preprocess.py

@@ -2618,6 +2618,14 @@ 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-',
+ usedefault=True,
+ desc='Direction in which slice_timing is specified (default: k). If negative,'
+ 'slice_timing is defined in reverse order, that is, the first entry '
+ 'corresponds to the slice with the largest index, and the final entry '
+ 'corresponds to slice index zero. Only in effect when slice_timing is '
+ 'passed as list, not when it is passed as file.',)
  rlt = traits.Bool(
  desc='Before shifting, remove the mean and linear trend',
  argstr='-rlt')
@@ -2660,6 +2668,17 @@ class TShift(AFNICommand):
  >>> tshift._list_outputs()['timing_file'] # doctest: +ELLIPSIS
  '.../slice_timing.1D'
 
+ >>> np.loadtxt(tshift._list_outputs()['timing_file']).tolist()[:5]
+ [0.0, 0.4, 0.8, 1.2, 1.6]
+
+ If ``slice_encoding_direction`` is set to ``'k-'``, the slice timing is reversed:
+
+ >>> tshift.inputs.slice_encoding_direction = 'k-'
+ >>> tshift.cmdline
+ '3dTshift -prefix functional_tshift -tpattern @slice_timing.1D -TR 2.5s -tzero 0.0 functional.nii'
+ >>> np.loadtxt(tshift._list_outputs()['timing_file']).tolist()[:5]
+ [15.6, 15.2, 14.8, 14.4, 14.0]
+
  This method creates a ``slice_timing.1D`` file to be passed to ``3dTshift``.
  A pre-existing slice-timing file may be used in the same way:
 
@@ -2723,9 +2742,13 @@ 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 = list(self.inputs.slice_timing)
+ if self.inputs.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):