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[ENH] added slice_encoding_direction input to TShift #2753

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Merged
merged 7 commits into from
Oct 26, 2018
Merged

[ENH] added slice_encoding_direction input to TShift #2753

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57ae723
added slice_encoding_direction input to TShift
fliem Oct 25, 2018
169e827
updated orcid
fliem Oct 25, 2018
3c7d0c2
better handle default values of slice_encoding_direction
fliem Oct 25, 2018
d67d660
docstring testing slice_encoding_direction
fliem Oct 25, 2018
daf1f25
remove bids reference from desc
fliem Oct 25, 2018
27c9448
FIX: Cast TraitList to a list
effigies Oct 25, 2018
27bbfc1
TEST: Print lists, not arrays
effigies Oct 25, 2018
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4 changes: 3 additions & 1 deletion .zenodo.json
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Original file line number Diff line number Diff line change
Expand Up @@ -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"
Expand Down
14 changes: 13 additions & 1 deletion nipype/interfaces/afni/preprocess.py
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Expand Up @@ -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')
Expand Down Expand Up @@ -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):
Expand Down