diff --git a/AFQ/api.py b/AFQ/api.py
index 76407d061..c46ca429c 100644
--- a/AFQ/api.py
+++ b/AFQ/api.py
@@ -442,7 +442,7 @@ def __init__(self,
                 bundle_names = BUNDLES
 
         # Create the bundle dict after reg_template has been resolved:
-        self.reg_template_img, _ = self._reg_img(self.reg_template)
+        self.reg_template_img, _ = self._reg_img(self.reg_template, False)
         self.bundle_dict = make_bundle_dict(bundle_names=bundle_names,
                                             seg_algo=self.seg_algo,
                                             resample_to=self.reg_template_img)
@@ -823,11 +823,10 @@ def _get_best_scalar(self):
                 return scalar
         return self.scalars[0]
 
-    def _reg_img(self, img, row=None):
+    def _reg_img(self, img, mask, row=None):
         if row is not None and row["reg_subject"] is not None:
-            return nib.load(row["reg_subject"]), None
-
-        if isinstance(img, str):
+            img = nib.load(row["reg_subject"])
+        elif isinstance(img, str):
             img_l = img.lower()
             if img_l == "mni_t2":
                 img = afd.read_mni_template(
@@ -868,13 +867,22 @@ def _reg_img(self, img, row=None):
             else:
                 img = nib.load(img)
 
+        if mask:
+            brain_mask_file = self._brain_mask(row)
+            brain_mask = nib.load(brain_mask_file).get_fdata().astype(bool)
+
+            masked_data = img.get_fdata()
+            masked_data[~brain_mask] = 0
+
+            img = nib.Nifti1Image(masked_data, img.affine)
+
         return img, None
 
     def _reg_prealign(self, row):
         prealign_file = self._get_fname(
             row, '_prealign_from-DWI_to-MNI_xfm.npy')
         if self.force_recompute or not op.exists(prealign_file):
-            reg_subject_img, _ = self._reg_img(self.reg_subject, row)
+            reg_subject_img, _ = self._reg_img(self.reg_subject, True, row)
             _, aff = reg.affine_registration(
                 reg_subject_img.get_fdata(),
                 self.reg_template_img.get_fdata(),
@@ -936,9 +944,9 @@ def _mapping(self, row):
                 reg_prealign = None
 
             reg_template_img, reg_template_sls = \
-                self._reg_img(self.reg_template, row)
+                self._reg_img(self.reg_template, False, row)
             reg_subject_img, reg_subject_sls = \
-                self._reg_img(self.reg_subject, row)
+                self._reg_img(self.reg_subject, True, row)
 
             start_time = time()
             if self.reg_algo == "slr":