FIX #3653: added option for using compressed files as inputs in CAT12 interface

Author: Oweda

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()
         ]