Merge pull request #1282 from satra/fix/freesurfer_T2

fix: ensure that T2 file gets used to clean surface

Author: satra

nipype/interfaces/freesurfer/preprocess.py

@@ -609,7 +609,9 @@ class ReconAllInputSpec(CommandLineInputSpec):
     T1_files = InputMultiPath(File(exists=True), argstr='-i %s...',
                               desc='name of T1 file to process')
     T2_file = File(exists=True, argstr="-T2 %s", min_ver='5.3.0',
-                   desc='Use a T2 image to refine the cortical surface')
+                   desc='Convert T2 image to orig directory')
+    use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0',
+                         desc='Use converted T2 to refine the cortical surface')
     openmp = traits.Int(argstr="-openmp %d",
                         desc="Number of processors to use in parallel")
     subjects_dir = Directory(exists=True, argstr='-sd %s', hash_files=False,

nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py

@@ -36,6 +36,9 @@ def test_ReconAll_inputs():
     ),
     terminal_output=dict(nohash=True,
     ),
+    use_T2=dict(argstr='-T2pial',
+    min_ver='5.3.0',
+    ),
     )
     inputs = ReconAll.input_spec()
 

nipype/interfaces/freesurfer/utils.py

@@ -360,7 +360,7 @@ def _list_outputs(self):
                 source = self.inputs.source_file
             else:
                 source = self.inputs.source_annot_file
-                
+
             # Some recon-all files don't have a proper extension (e.g. "lh.thickness")
             # so we have to account for that here
             bad_extensions = [".%s" % e for e in ["area", "mid", "pial", "avg_curv", "curv", "inflated",