Merge pull request #3652 from bogpetre/master

ENH: FILMGLS gifti output support in surface mode

Author: effigies

.zenodo.json

@@ -924,6 +924,11 @@
       "affiliation": "MIT, HMS",
       "name": "Ghosh, Satrajit",
       "orcid": "0000-0002-5312-6729"
+    },
+    {
+      "affiliation": "Department of Psychological and Brain Sciences, Dartmouth College",
+      "name": "Petre, Bogdan",
+      "orcid": "0000-0002-8437-168X"
     }
   ],
   "keywords": [

nipype/interfaces/fsl/base.py

@@ -57,6 +57,7 @@ class Info(PackageInfo):
         "NIFTI_PAIR": ".img",
         "NIFTI_GZ": ".nii.gz",
         "NIFTI_PAIR_GZ": ".img.gz",
+        "GIFTI": ".func.gii",
     }
 
     if os.getenv("FSLDIR"):
@@ -72,8 +73,8 @@ def output_type_to_ext(cls, output_type):
 
         Parameters
         ----------
-        output_type : {'NIFTI', 'NIFTI_GZ', 'NIFTI_PAIR', 'NIFTI_PAIR_GZ'}
-            String specifying the output type.
+        output_type : {'NIFTI', 'NIFTI_GZ', 'NIFTI_PAIR', 'NIFTI_PAIR_GZ', 'GIFTI'}
+            String specifying the output type. Note: limited GIFTI support.
 
         Returns
         -------

nipype/interfaces/fsl/model.py

@@ -812,12 +812,20 @@ class FILMGLS(FSLCommand):
     _cmd = "film_gls"
     input_spec = FILMGLSInputSpec
     output_spec = FILMGLSOutputSpec
+
     if Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.6"):
         input_spec = FILMGLSInputSpec507
         output_spec = FILMGLSOutputSpec507
     elif Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.4"):
         input_spec = FILMGLSInputSpec505
 
+    def __init__(self, **inputs):
+        super(FILMGLS, self).__init__(**inputs)
+        if Info.version() and LooseVersion(Info.version()) > LooseVersion("5.0.6"):
+            if 'output_type' not in inputs:
+                if isdefined(self.inputs.mode) and self.inputs.mode == 'surface':
+                    self.inputs.output_type = 'GIFTI'
+
     def _get_pe_files(self, cwd):
         files = None
         if isdefined(self.inputs.design_file):