ENH: Enable recon-all -FLAIR/-FLAIRpial

Author: effigies

nipype/interfaces/freesurfer/preprocess.py

@@ -628,10 +628,17 @@ class ReconAllInputSpec(CommandLineInputSpec):
  argstr="-hemi %s")
  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',
+ T2_file = File(exists=True, argstr="-T2 %s",
+ min_ver='5.3.0', xor=['FLAIR_file'],
  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')
+ FLAIR_file = File(exists=True, argstr="-FLAIR %s",
+ min_ver='5.3.0', xor=['T2_file'],
+ desc='Convert FLAIR image to orig directory')
+ use_T2 = traits.Bool(argstr="-T2pial", min_ver='5.3.0', xor=['use_FLAIR'],
+ desc='Use T2 image to refine the pial surface')
+ use_FLAIR = traits.Bool(argstr="-FLAIRpial",
+ min_ver='5.3.0', xor=['use_T2'],
+ desc='Use FLAIR image to refine the pial surface')
  openmp = traits.Int(argstr="-openmp %d",
  desc="Number of processors to use in parallel")
  parallel = traits.Bool(argstr="-parallel",