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[FIX] small edits to my previous pull request (PR #3394) due to bugs revealed when running within my nipype workflow #3396

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Merged
merged 3 commits into from
Oct 25, 2021
Merged

[FIX] small edits to my previous pull request (PR #3394) due to bugs revealed when running within my nipype workflow #3396

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f525c94
corrected some bugs by testing within our workflow
Oct 22, 2021
5991172
Merge branch 'master' of github.com:fabioboh/nipype
Oct 22, 2021
f4691be
formatting
Oct 22, 2021
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5 changes: 2 additions & 3 deletions nipype/interfaces/spm/preprocess.py
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Original file line number Diff line number Diff line change
Expand Up @@ -339,18 +339,17 @@ def _format_arg(self, opt, spec, val):

if opt in ["in_files", "vdmfile"]:
return scans_for_fname(ensure_list(val))
return super(FieldMap, self)._format_arg(opt, spec, val)
return super(ApplyVDM, self)._format_arg(opt, spec, val)

def _parse_inputs(self):
"""validate spm fieldmap options if set to None ignore"""

einputs = super(ApplyVDM, self)._parse_inputs()

return [{"applymap": einputs[0]}]
return [{"applyvdm": einputs[0]}]

def _list_outputs(self):
outputs = self._outputs().get()
jobtype = self.inputs.jobtype
resliced_all = self.inputs.write_which[0] > 0
resliced_mean = self.inputs.write_which[1] > 0
if resliced_mean:
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