Merge pull request #1493 from mattfeld/master

ENH Added grad_dev input to fsl.dti.bedpostx5 interface

Author: satra

CHANGES

@@ -1,6 +1,7 @@
 Release 0.12.0-rc1 (April 20, 2016)
 ============
 
+* ENH: Added grad_dev input to fsl.dti.bedpostx5 interface(https://github.com/nipy/nipype/pull/1493)
 * ENH: ResourceMultiProc plugin to support resource allocation (https://github.com/nipy/nipype/pull/1372)
 * ENH: Added dcm2niix interface (https://github.com/nipy/nipype/pull/1435)
 * ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)

nipype/interfaces/fsl/dti.py

@@ -265,6 +265,7 @@ class BEDPOSTX5InputSpec(FSLXCommandInputSpec):
                         usedefault=True, position=1, argstr='%s')
     gradnonlin = traits.Bool(False, argstr='-g', desc=('consider gradient '
                                                        'nonlinearities, default off'))
+    grad_dev = File(exists=True, desc='grad_dev file, if gradnonlin, -g is True')
     use_gpu = traits.Bool(False, desc='Use the GPU version of bedpostx')
 
 
@@ -348,6 +349,10 @@ def _run_interface(self, runtime):
                  os.path.join(subjectdir, 'bvals'))
         copyfile(self.inputs.bvecs,
                  os.path.join(subjectdir, 'bvecs'))
+        if isdefined(self.inputs.grad_dev):
+            _, _, ext = split_filename(self.inputs.grad_dev)
+            copyfile(self.inputs.grad_dev,
+                     os.path.join(subjectdir, 'grad_dev' + ext))
 
         retval = super(BEDPOSTX5, self)._run_interface(runtime)
 

nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py

@@ -36,6 +36,7 @@ def test_BEDPOSTX5_inputs():
     ),
     fudge=dict(argstr='-w %d',
     ),
+    grad_dev=dict(),
     gradnonlin=dict(argstr='-g',
     ),
     ignore_exception=dict(nohash=True,