fsl_glm interface

Author: bpinsard

nipype/interfaces/fsl/model.py

@@ -1518,3 +1518,57 @@ def _list_outputs(self):
                 '%s_%s_corrp_fstat*.nii'%(self.inputs.base_name,prefix)))
 
         return outputs
+
+
+class GLMInputSpec(FSLCommandInputSpec):
+    in_file = File(
+        exists=True,mandatory=True,
+        argstr='-i %s',
+        desc='input 3d+t file',)
+    design = File(
+        exists=True, mandatory=True,
+        argstr='-d %s',
+        desc='design file or image file')
+    out_file = File(
+        genfile=True, argstr="-o %s",
+        desc="file or image output")
+    mask = File(
+        exists=True,
+        argstr='-m %s',
+        desc='mask file')
+    contrasts = File(
+        exists=True,
+        argstr='-c %s',
+        desc='t-contrasts file')
+    options = traits.String(
+        argstr='%s',
+        desc = 'fsl_glm options')
+class GLMOutputSpec(TraitedSpec):
+    out_file = File(
+        exists=True,
+        desc = 'file or image output')
+
+class GLM(FSLCommand):
+    _cmd = 'fsl_glm'
+    input_spec = GLMInputSpec
+    output_spec = GLMOutputSpec
+
+    def _list_outputs(self):
+        outputs = self.output_spec().get()
+        outputs['out_file'] = self.inputs.out_file
+        # Generate an out_file if one is not provided
+        if not isdefined(outputs['out_file']) and isdefined(self.inputs.in_file):
+            ext = Info.output_type_to_ext(self.inputs.output_type)
+            if split_filename(self.inputs.in_file)[-1] in Info.ftypes.values():
+                ext = '.txt'
+            outputs['out_file'] = self._gen_fname(self.inputs.in_file,
+                                                  suffix='_glm',
+                                                  ext=ext)
+
+        return outputs
+
+    def _gen_filename(self, name):
+        if name in ('out_file'):
+            return self._list_outputs()[name]
+        else:
+            return None