diff --git a/qsiprep/data/pipelines/pyafq_tractometry.json b/qsiprep/data/pipelines/pyafq_tractometry.json
index cf50e428..40acf80d 100644
--- a/qsiprep/data/pipelines/pyafq_tractometry.json
+++ b/qsiprep/data/pipelines/pyafq_tractometry.json
@@ -16,13 +16,13 @@
                 "directions": "prob",
                 "max_angle": 30.0,
                 "sphere": "",
-                "seed_mask": "",
-                "seed_threshold": 0,
+                "seed_mask": "WM_probseg",
+                "seed_threshold": 0.5,
                 "n_seeds": 1,
                 "random_seeds": false,
                 "rng_seed": "",
-                "stop_mask": "",
-                "stop_threshold": 0,
+                "stop_mask": "WM_probseg",
+                "stop_threshold": 0.5,
                 "step_size": 0.5,
                 "min_length": 50,
                 "max_length": 250,
@@ -67,7 +67,6 @@
                 "csd_lambda_": 1,
                 "csd_tau": 0.1,
                 "gtol": 0.01,
-                "brain_mask_definition": "",
                 "bundle_info": "",
                 "reg_template_spec": "mni_T1",
                 "mapping_definition": "",
diff --git a/qsiprep/interfaces/pyafq.py b/qsiprep/interfaces/pyafq.py
index 33156fa1..2cc01f17 100644
--- a/qsiprep/interfaces/pyafq.py
+++ b/qsiprep/interfaces/pyafq.py
@@ -30,6 +30,7 @@ class PyAFQInputSpec(BaseInterfaceInputSpec):
     bvec_file = File(exists=True, mandatory=True)
     dwi_file = File(exists=True, mandatory=True)
     mask_file = File(exists=True, mandatory=True)
+    wm_mask_file = File(exists=True, mandatory=True)
     itk_file = File(exists=True, mandatory=True)
     kwargs = traits.Dict(exists=True, mandatory=True)
     tck_file = traits.Either(None, File(exists=True))
@@ -56,6 +57,8 @@ def _run_interface(self, runtime):
                                    newpath=shim_dir)
         mask_file = fname_presuffix(self.inputs.mask_file,
                                     newpath=shim_dir)
+        wm_mask_file = fname_presuffix(self.inputs.wm_mask_file,
+                                       newpath=shim_dir)
         itk_file = fname_presuffix(self.inputs.itk_file,
                                    newpath=shim_dir)
         os.symlink(self.inputs.bval_file, bval_file)
@@ -63,24 +66,35 @@ def _run_interface(self, runtime):
         os.symlink(self.inputs.dwi_file, dwi_file)
         os.symlink(self.inputs.mask_file, mask_file)
         os.symlink(self.inputs.itk_file, itk_file)
-
+        os.symlink(self.inputs.wm_mask_file, wm_mask_file)
         kwargs = self.inputs.kwargs
 
         if self.inputs.tck_file and isdefined(self.inputs.tck_file):
             tck_file = fname_presuffix(self.inputs.tck_file,
-                                    newpath=shim_dir)
+                                       newpath=shim_dir)
             os.symlink(self.inputs.tck_file, tck_file)
         else:
             tck_file = None
+
         brain_mask_definition = ImageFile(path=mask_file)
-        itk_map = ItkMap(warp_path=itk_file)
+        seed_mask_definition = ImageFile(path=wm_mask_file)
+        stop_mask_definition = ImageFile(path=wm_mask_file)
+
+        # XXX Make ItkMap work at some point
+        # itk_map = ItkMap(warp_path=itk_file)
 
         if tck_file is None:
             tck_file = kwargs['import_tract']
         kwargs.pop('import_tract', None)
-        if brain_mask_definition is None:
-            brain_mask_definition = kwargs['brain_mask_definition']
         kwargs.pop('brain_mask_definition', None)
+
+        tracking_params = kwargs.pop('tracking_params', None)
+        if tracking_params is not None:
+            if tracking_params["seed_mask"] == "WM_prob":
+                tracking_params["seed_mask"] = seed_mask_definition
+            if tracking_params["stop_mask"] == "WM_prob":
+                tracking_params["stop_mask"] = stop_mask_definition
+
         # if itk_map is None:  # Use pyAFQ internal mapping
         #     itk_map = kwargs['mapping_definition']
         # kwargs.pop('mapping_definition', None)
@@ -100,6 +114,7 @@ def _run_interface(self, runtime):
             import_tract=tck_file,
             brain_mask_definition=brain_mask_definition,
             # mapping_definition=itk_map,
+            tracking_params=tracking_params,
             **kwargs)
 
         if "export" not in kwargs or kwargs["export"] == "all":
diff --git a/qsiprep/workflows/recon/pyafq.py b/qsiprep/workflows/recon/pyafq.py
index 5d3f7a5f..b3916cc5 100644
--- a/qsiprep/workflows/recon/pyafq.py
+++ b/qsiprep/workflows/recon/pyafq.py
@@ -79,6 +79,7 @@ def init_pyafq_wf(omp_nthreads, available_anatomical_data,
             ('bval_file', 'bval_file'),
             ('bvec_file', 'bvec_file'),
             ('dwi_mask', 'mask_file'),
+            ('wm_mask', 'wm_mask_file'),
             ('t1_2_mni_reverse_transform', 'itk_file')]),
         (run_afq, outputnode, [('afq_dir', 'afq_dir')])
     ])