enh: update possible extensions

Author: mgxd

nipype/interfaces/dcm2nii.py

@@ -330,7 +330,7 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
         False,
         argstr='-t',
         usedefault=True,
-        desc="Flag if text notes include private patient details")
+        desc="Text notes including private patient details")
     compression = traits.Enum(
         1, 2, 3, 4, 5, 6, 7, 8, 9,
         argstr='-%d',
@@ -348,6 +348,9 @@ class Dcm2niixInputSpec(CommandLineInputSpec):
     philips_float = traits.Bool(
         argstr='-p',
         desc="Philips precise float (not display) scaling")
+    to_nrrd = traits.Bool(
+        argstr="-e",
+        desc="Export as NRRD instead of NIfTI")
 
 
 class Dcm2niixOutputSpec(TraitedSpec):
@@ -395,8 +398,11 @@ def version(self):
         return Info.version()
 
     def _format_arg(self, opt, spec, val):
-        bools = ['bids_format', 'merge_imgs', 'single_file', 'verbose', 'crop',
-                 'has_private', 'anon_bids', 'ignore_deriv', 'philips_float']
+        bools = [
+            'bids_format', 'merge_imgs', 'single_file', 'verbose', 'crop',
+            'has_private', 'anon_bids', 'ignore_deriv', 'philips_float',
+            'to_nrrd',
+        ]
         if opt in bools:
             spec = deepcopy(spec)
             if val:
@@ -425,17 +431,27 @@ def _parse_stdout(self, stdout):
 
     def _parse_files(self, filenames):
         outfiles, bvals, bvecs, bids = [], [], [], []
-        outtypes = (".nii", ".nii.gz", ".bval", ".bvec", ".json")
+        outtypes = [".gz", ".bval", ".bvec", ".json", ".txt"]
+        if self.to_nrrd:
+            outtypes += [".nrrd", ".nhdr"]
+        else:
+            outtypes += [".nii"]
+
         for filename in filenames:
             # search for relevant files, and sort accordingly
             for fl in search_files(filename, outtypes):
-                if fl.endswith(".nii") or fl.endswith(".gz"):
+                if (
+                    fl.endswith(".nii") or
+                    fl.endswith(".gz") or
+                    fl.endswith(".nrrd") or
+                    fl.endswith(".nhdr")
+                ):
                     outfiles.append(fl)
                 elif fl.endswith(".bval"):
                     bvals.append(fl)
                 elif fl.endswith(".bvec"):
                     bvecs.append(fl)
-                elif fl.endswith(".json"):
+                elif fl.endswith(".json") or fl.endswith(".txt"):
                     bids.append(fl)
         self.output_files = outfiles
         self.bvecs = bvecs

nipype/interfaces/tests/test_auto_Dcm2niix.py

@@ -61,6 +61,7 @@ def test_Dcm2niix_inputs():
             position=-1,
             xor=['source_dir'],
         ),
+        to_nrrd=dict(argstr='-e', ),
         verbose=dict(
             argstr='-v',
             usedefault=True,