FIX nipy#3653: added option for using compressed files as inputs in C…

…AT12 interface

nipype/interfaces/cat12/preprocess.py

@@ -8,6 +8,7 @@
  isdefined,
  File,
  Str,
+ ImageFile,
 )
 from nipype.interfaces.cat12.base import Cell
 
@@ -23,7 +24,7 @@
 
 class CAT12SegmentInputSpec(SPMCommandInputSpec):
  in_files = InputMultiPath(
- ImageFileSPM(exists=True),
+ ImageFile(exists=True),
  field="data",
  desc="file to segment",
  mandatory=True,
@@ -559,6 +560,8 @@ def _format_arg(self, opt, spec, val):
  """Convert input to appropriate format for spm"""
  if opt == "in_files":
  if isinstance(val, list):
+ if '.nii.gz' in val[0]:
+ return scans_for_fnames(val, keep4d=True)
  return scans_for_fnames(val)
  else:
  return scans_for_fname(val)
@@ -571,7 +574,8 @@ def _list_outputs(self):
  outputs = self._outputs().get()
  f = self.inputs.in_files[0]
  pth, base, ext = split_filename(f)
-
+ if '.nii.gz' in f:
+ f = f[:-3]
  outputs["mri_images"] = [
  str(mri) for mri in Path(pth).glob("mri/*") if mri.is_file()
  ]