diff --git a/scripts/scil_bundle_compute_centroid.py b/scripts/scil_bundle_compute_centroid.py
index 19adb053c..97af1869b 100755
--- a/scripts/scil_bundle_compute_centroid.py
+++ b/scripts/scil_bundle_compute_centroid.py
@@ -46,7 +46,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundle)
+    assert_inputs_exist(parser, args.in_bundle, args.reference)
     assert_outputs_exist(parser, args, args.out_centroid)
 
     if args.nb_points < 2:
diff --git a/scripts/scil_bundle_diameter.py b/scripts/scil_bundle_diameter.py
index 9be91fed4..7b9cfb72e 100755
--- a/scripts/scil_bundle_diameter.py
+++ b/scripts/scil_bundle_diameter.py
@@ -213,7 +213,8 @@ def main():
     tmp = args.in_bundles + args.in_labels
     args.in_labels = args.in_bundles[(len(tmp) // 2):] + args.in_labels
     args.in_bundles = args.in_bundles[0:len(tmp) // 2]
-    assert_inputs_exist(parser, args.in_bundles+args.in_labels)
+    assert_inputs_exist(parser, args.in_bundles + args.in_labels,
+                        args.reference)
     assert_output_dirs_exist_and_empty(parser, args, [],
                                        optional=args.save_rendering)
 
diff --git a/scripts/scil_bundle_filter_by_occurence.py b/scripts/scil_bundle_filter_by_occurence.py
index f7116578f..2f24278e5 100755
--- a/scripts/scil_bundle_filter_by_occurence.py
+++ b/scripts/scil_bundle_filter_by_occurence.py
@@ -70,7 +70,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     output_streamlines_filename = '{}streamlines.trk'.format(
         args.output_prefix)
     output_voxels_filename = '{}voxels.nii.gz'.format(args.output_prefix)
diff --git a/scripts/scil_bundle_generate_priors.py b/scripts/scil_bundle_generate_priors.py
index fb2f18773..3c503670a 100755
--- a/scripts/scil_bundle_generate_priors.py
+++ b/scripts/scil_bundle_generate_priors.py
@@ -78,8 +78,8 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     required = [args.in_bundle, args.in_fodf, args.in_mask]
-    assert_inputs_exist(parser, required)
-    assert_headers_compatible(parser, required)
+    assert_inputs_exist(parser, required, args.reference)
+    assert_headers_compatible(parser, required, reference=args.reference)
 
     out_efod = os.path.join(args.out_dir,
                             '{0}efod.nii.gz'.format(args.out_prefix))
diff --git a/scripts/scil_bundle_mean_fixel_afd.py b/scripts/scil_bundle_mean_fixel_afd.py
index 8cdd859a9..7b401ceb2 100755
--- a/scripts/scil_bundle_mean_fixel_afd.py
+++ b/scripts/scil_bundle_mean_fixel_afd.py
@@ -63,7 +63,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_bundle, args.in_fodf])
+    assert_inputs_exist(parser, [args.in_bundle, args.in_fodf],
+                        args.reference)
     assert_outputs_exist(parser, args, [args.afd_mean_map])
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)
diff --git a/scripts/scil_bundle_mean_fixel_bingham_metric.py b/scripts/scil_bundle_mean_fixel_bingham_metric.py
index 469dc3abc..a025ecc42 100755
--- a/scripts/scil_bundle_mean_fixel_bingham_metric.py
+++ b/scripts/scil_bundle_mean_fixel_bingham_metric.py
@@ -73,9 +73,9 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_bundle,
-                                 args.in_bingham,
-                                 args.in_bingham_metric])
+    assert_inputs_exist(parser, [args.in_bundle, args.in_bingham,
+                                 args.in_bingham_metric],
+                        args.reference)
     assert_outputs_exist(parser, args, [args.out_mean_map])
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)
diff --git a/scripts/scil_bundle_pairwise_comparison.py b/scripts/scil_bundle_pairwise_comparison.py
index dc4961ad8..0d46cf4c5 100755
--- a/scripts/scil_bundle_pairwise_comparison.py
+++ b/scripts/scil_bundle_pairwise_comparison.py
@@ -286,7 +286,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, [args.out_json])
 
     if args.ratio and not args.single_compare:
diff --git a/scripts/scil_bundle_score_many_bundles_one_tractogram.py b/scripts/scil_bundle_score_many_bundles_one_tractogram.py
index cf29f4505..365c2c993 100755
--- a/scripts/scil_bundle_score_many_bundles_one_tractogram.py
+++ b/scripts/scil_bundle_score_many_bundles_one_tractogram.py
@@ -94,7 +94,7 @@ def _build_arg_parser():
 
 def load_and_verify_everything(parser, args):
 
-    assert_inputs_exist(parser, [args.gt_config])
+    assert_inputs_exist(parser, args.gt_config, args.reference)
     if not os.path.isdir(args.bundles_dir):
         parser.error("Bundles dir ({}) does not exist."
                      .format(args.bundles_dir))
diff --git a/scripts/scil_bundle_score_same_bundle_many_segmentations.py b/scripts/scil_bundle_score_same_bundle_many_segmentations.py
index 16dc43348..8e246e2c9 100755
--- a/scripts/scil_bundle_score_same_bundle_many_segmentations.py
+++ b/scripts/scil_bundle_score_same_bundle_many_segmentations.py
@@ -159,7 +159,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, args.out_json)
 
     if (not args.streamlines_measures) and (not args.voxels_measures):
diff --git a/scripts/scil_bundle_shape_measures.py b/scripts/scil_bundle_shape_measures.py
index 1f9928a4c..0aa1c5ddf 100755
--- a/scripts/scil_bundle_shape_measures.py
+++ b/scripts/scil_bundle_shape_measures.py
@@ -199,7 +199,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, [], args.out_json)
 
     nbr_cpu = validate_nbr_processes(parser, args)
diff --git a/scripts/scil_clean_qbx_clusters.py b/scripts/scil_clean_qbx_clusters.py
index 5a973d78a..3f3f45ec2 100755
--- a/scripts/scil_clean_qbx_clusters.py
+++ b/scripts/scil_clean_qbx_clusters.py
@@ -151,7 +151,7 @@ def keypress_callback(obj, _):
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles)
+    assert_inputs_exist(parser, args.in_bundles, args.reference)
     assert_outputs_exist(parser, args, [args.out_accepted, args.out_rejected])
 
     if args.out_accepted_dir:
diff --git a/scripts/scil_header_validate_compatibility.py b/scripts/scil_header_validate_compatibility.py
index 442d464f5..390b197a9 100755
--- a/scripts/scil_header_validate_compatibility.py
+++ b/scripts/scil_header_validate_compatibility.py
@@ -38,7 +38,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_files)
+    assert_inputs_exist(parser, args.in_files, args.reference)
     assert_headers_compatible(parser, args.in_files,
                               verbose_all_compatible=True,
                               reference=args.reference)
diff --git a/scripts/scil_lesions_info.py b/scripts/scil_lesions_info.py
index cb3e947cf..b23fff541 100755
--- a/scripts/scil_lesions_info.py
+++ b/scripts/scil_lesions_info.py
@@ -81,7 +81,7 @@ def main():
 
     assert_inputs_exist(parser, [args.in_lesion],
                         optional=[args.bundle, args.bundle_mask,
-                                  args.bundle_labels_map])
+                                  args.bundle_labels_map, args.reference])
     assert_outputs_exist(parser, args, args.out_json,
                          optional=[args.out_lesion_stats,
                                    args.out_streamlines_stats])
diff --git a/scripts/scil_outlier_rejection.py b/scripts/scil_outlier_rejection.py
index 977df8ad6..c2de9ba8d 100755
--- a/scripts/scil_outlier_rejection.py
+++ b/scripts/scil_outlier_rejection.py
@@ -53,7 +53,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundle)
+    assert_inputs_exist(parser, args.in_bundle, args.reference)
     assert_outputs_exist(parser, args, args.out_bundle, args.remaining_bundle)
     if args.alpha <= 0 or args.alpha > 1:
         parser.error('--alpha should be ]0, 1]')
diff --git a/scripts/scil_score_tractogram.py b/scripts/scil_score_tractogram.py
index 77301db54..0846d5561 100755
--- a/scripts/scil_score_tractogram.py
+++ b/scripts/scil_score_tractogram.py
@@ -173,7 +173,7 @@ def load_and_verify_everything(parser, args):
     args.json_prefix = os.path.join(args.out_dir, args.json_prefix)
     json_outputs = [args.json_prefix + 'processing_stats.json',
                     args.json_prefix + 'results.json']
-    assert_inputs_exist(parser, args.gt_config)
+    assert_inputs_exist(parser, args.gt_config, args.reference)
     assert_output_dirs_exist_and_empty(parser, args, args.out_dir,
                                        create_dir=True)
     assert_outputs_exist(parser, args, json_outputs)
diff --git a/scripts/scil_tractogram_apply_transform.py b/scripts/scil_tractogram_apply_transform.py
index fd2b764a0..574a16297 100755
--- a/scripts/scil_tractogram_apply_transform.py
+++ b/scripts/scil_tractogram_apply_transform.py
@@ -105,7 +105,8 @@ def main():
 
     assert_inputs_exist(parser, [args.in_moving_tractogram,
                                  args.in_target_file,
-                                 args.in_transfo], args.in_deformation)
+                                 args.in_transfo],
+                        [args.in_deformation, args.reference])
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     args.bbox_check = False  # Adding manually bbox_check argument.
diff --git a/scripts/scil_tractogram_apply_transform_to_hdf5.py b/scripts/scil_tractogram_apply_transform_to_hdf5.py
index 9affc33c5..054d2d06b 100755
--- a/scripts/scil_tractogram_apply_transform_to_hdf5.py
+++ b/scripts/scil_tractogram_apply_transform_to_hdf5.py
@@ -71,7 +71,8 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.in_hdf5, args.in_target_file,
-                                 args.in_transfo], args.in_deformation)
+                                 args.in_transfo],
+                        [args.in_deformation, args.reference])
     assert_outputs_exist(parser, args, args.out_hdf5)
 
     # HDF5 will not overwrite the file
diff --git a/scripts/scil_tractogram_assign_custom_color.py b/scripts/scil_tractogram_assign_custom_color.py
index 74b936f12..ce8121407 100755
--- a/scripts/scil_tractogram_assign_custom_color.py
+++ b/scripts/scil_tractogram_assign_custom_color.py
@@ -172,7 +172,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.out_colorbar)
 
diff --git a/scripts/scil_tractogram_assign_uniform_color.py b/scripts/scil_tractogram_assign_uniform_color.py
index 420ee645e..8e5e45007 100755
--- a/scripts/scil_tractogram_assign_uniform_color.py
+++ b/scripts/scil_tractogram_assign_uniform_color.py
@@ -70,7 +70,7 @@ def main():
     if len(args.in_tractograms) > 1 and args.out_tractogram:
         parser.error('Using multiple inputs, use --out_suffix.')
 
-    assert_inputs_exist(parser, args.in_tractograms)
+    assert_inputs_exist(parser, args.in_tractograms, args.reference)
 
     if args.out_suffix:
         if args.out_tractogram:
diff --git a/scripts/scil_tractogram_cut_streamlines.py b/scripts/scil_tractogram_cut_streamlines.py
index 81316eb7a..9cb341838 100755
--- a/scripts/scil_tractogram_cut_streamlines.py
+++ b/scripts/scil_tractogram_cut_streamlines.py
@@ -73,7 +73,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_tractogram, args.in_mask])
+    assert_inputs_exist(parser, [args.in_tractogram, args.in_mask],
+                        args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
     assert_headers_compatible(parser, [args.in_tractogram, args.in_mask],
                               reference=args.reference)
diff --git a/scripts/scil_tractogram_detect_loops.py b/scripts/scil_tractogram_detect_loops.py
index 8dd119c4b..921fc696e 100755
--- a/scripts/scil_tractogram_detect_loops.py
+++ b/scripts/scil_tractogram_detect_loops.py
@@ -80,7 +80,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.looping_tractogram)
     check_tracts_same_format(parser, [args.in_tractogram, args.out_tractogram,
diff --git a/scripts/scil_tractogram_dpp_math.py b/scripts/scil_tractogram_dpp_math.py
index 54e3a6a07..d60c8d5cf 100755
--- a/scripts/scil_tractogram_dpp_math.py
+++ b/scripts/scil_tractogram_dpp_math.py
@@ -106,7 +106,7 @@ def main():
     if args.verbose:
         logging.getLogger().setLevel(logging.INFO)
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     # Load the input files.
diff --git a/scripts/scil_tractogram_extract_ushape.py b/scripts/scil_tractogram_extract_ushape.py
index 54b7b9ee2..be98a694b 100755
--- a/scripts/scil_tractogram_extract_ushape.py
+++ b/scripts/scil_tractogram_extract_ushape.py
@@ -65,7 +65,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.remaining_tractogram)
     check_tracts_same_format(parser, [args.in_tractogram, args.out_tractogram,
diff --git a/scripts/scil_tractogram_filter_by_anatomy.py b/scripts/scil_tractogram_filter_by_anatomy.py
index 9542e2e82..f1a6372d0 100755
--- a/scripts/scil_tractogram_filter_by_anatomy.py
+++ b/scripts/scil_tractogram_filter_by_anatomy.py
@@ -277,7 +277,7 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.in_tractogram, args.in_wmparc],
-                        args.csf_bin)
+                        [args.csf_bin, args.reference])
     assert_output_dirs_exist_and_empty(parser, args, args.out_path,
                                        create_dir=True)
     assert_headers_compatible(parser, [args.in_tractogram, args.in_wmparc],
diff --git a/scripts/scil_tractogram_filter_by_length.py b/scripts/scil_tractogram_filter_by_length.py
index 0ba977460..d107d53fd 100755
--- a/scripts/scil_tractogram_filter_by_length.py
+++ b/scripts/scil_tractogram_filter_by_length.py
@@ -56,7 +56,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     if args.minL == 0 and np.isinf(args.maxL):
diff --git a/scripts/scil_tractogram_filter_by_orientation.py b/scripts/scil_tractogram_filter_by_orientation.py
index 0af0b652e..250f2a29a 100755
--- a/scripts/scil_tractogram_filter_by_orientation.py
+++ b/scripts/scil_tractogram_filter_by_orientation.py
@@ -88,7 +88,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram, args.save_rejected)
 
     if args.min_x == 0 and np.isinf(args.max_x) and \
diff --git a/scripts/scil_tractogram_filter_by_roi.py b/scripts/scil_tractogram_filter_by_roi.py
index 8545e14ec..ead346741 100755
--- a/scripts/scil_tractogram_filter_by_roi.py
+++ b/scripts/scil_tractogram_filter_by_roi.py
@@ -242,7 +242,7 @@ def main():
 
     # Todo. Prepare now the names of other files (ex, ROI) and verify if
     #  exist and compatible.
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram, args.save_rejected)
 
     if overwrite_distance:
diff --git a/scripts/scil_tractogram_flip.py b/scripts/scil_tractogram_flip.py
index a95449fd1..8eacb2caf 100755
--- a/scripts/scil_tractogram_flip.py
+++ b/scripts/scil_tractogram_flip.py
@@ -51,7 +51,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
diff --git a/scripts/scil_tractogram_math.py b/scripts/scil_tractogram_math.py
index 0feb70fd0..4bda43963 100755
--- a/scripts/scil_tractogram_math.py
+++ b/scripts/scil_tractogram_math.py
@@ -113,7 +113,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractograms)
+    assert_inputs_exist(parser, args.in_tractograms, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram,
                          optional=args.save_indices)
 
diff --git a/scripts/scil_tractogram_print_info.py b/scripts/scil_tractogram_print_info.py
index 48e604d29..f093b26d3 100755
--- a/scripts/scil_tractogram_print_info.py
+++ b/scripts/scil_tractogram_print_info.py
@@ -47,7 +47,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
 
diff --git a/scripts/scil_tractogram_project_map_to_streamlines.py b/scripts/scil_tractogram_project_map_to_streamlines.py
index eb0f7370b..97e33e344 100755
--- a/scripts/scil_tractogram_project_map_to_streamlines.py
+++ b/scripts/scil_tractogram_project_map_to_streamlines.py
@@ -87,8 +87,8 @@ def main():
     parser = _build_arg_parser()
     args = parser.parse_args()
 
-    assert_inputs_exist(parser, [args.in_tractogram] + args.in_maps)
-
+    assert_inputs_exist(parser, [args.in_tractogram] + args.in_maps,
+                        args.reference)
     assert_outputs_exist(parser, args, [args.out_tractogram])
 
     if args.verbose:
diff --git a/scripts/scil_tractogram_project_streamlines_to_map.py b/scripts/scil_tractogram_project_streamlines_to_map.py
index d128f3c3a..59f45d53e 100755
--- a/scripts/scil_tractogram_project_streamlines_to_map.py
+++ b/scripts/scil_tractogram_project_streamlines_to_map.py
@@ -173,7 +173,7 @@ def main():
 
     # -------- General checks ----------
     assert_inputs_exist(parser, [args.in_bundle],
-                        args.load_dps + args.load_dpp)
+                        args.load_dps + args.load_dpp + [args.reference])
 
     # Find all final output files (one per metric).
     if args.load_dps or args.load_dpp:
diff --git a/scripts/scil_tractogram_qbx.py b/scripts/scil_tractogram_qbx.py
index fdc8da4a0..b90f9bdff 100755
--- a/scripts/scil_tractogram_qbx.py
+++ b/scripts/scil_tractogram_qbx.py
@@ -58,7 +58,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, [], optional=args.out_centroids)
     assert_output_dirs_exist_and_empty(parser, args,
                                        args.out_clusters_dir,
diff --git a/scripts/scil_tractogram_register.py b/scripts/scil_tractogram_register.py
index c8e467a54..21f0312a7 100755
--- a/scripts/scil_tractogram_register.py
+++ b/scripts/scil_tractogram_register.py
@@ -63,7 +63,9 @@ def main():
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
     assert_inputs_exist(parser, [args.moving_tractogram,
-                                 args.static_tractogram])
+                                 args.static_tractogram],
+                        [args.moving_tractogram_ref,
+                         args.static_tractogram_ref])
 
     if args.only_rigid:
         matrix_filename = os.path.splitext(args.out_name)[0] + '_rigid.txt'
diff --git a/scripts/scil_tractogram_resample.py b/scripts/scil_tractogram_resample.py
index f00c01eb2..7375cbba2 100755
--- a/scripts/scil_tractogram_resample.py
+++ b/scripts/scil_tractogram_resample.py
@@ -122,7 +122,7 @@ def main():
              args.streamline_wise_std <= 0):
         parser.error('STD needs to be above 0.')
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     logging.info("Loading sft.")
diff --git a/scripts/scil_tractogram_resample_nb_points.py b/scripts/scil_tractogram_resample_nb_points.py
index 5cd3e5a2b..441a5a1fc 100755
--- a/scripts/scil_tractogram_resample_nb_points.py
+++ b/scripts/scil_tractogram_resample_nb_points.py
@@ -49,7 +49,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
diff --git a/scripts/scil_tractogram_segment_bundles.py b/scripts/scil_tractogram_segment_bundles.py
index 790004cd9..f0ebf3153 100755
--- a/scripts/scil_tractogram_segment_bundles.py
+++ b/scripts/scil_tractogram_segment_bundles.py
@@ -101,8 +101,8 @@ def main():
                                                     args.in_directory, x))]
 
     assert_inputs_exist(parser, args.in_tractograms +
-                        [args.in_config_file,
-                         args.in_transfo])
+                        [args.in_config_file, args.in_transfo],
+                        args.reference)
 
     for in_tractogram in args.in_tractograms:
         ext = os.path.splitext(in_tractogram)[1]
diff --git a/scripts/scil_tractogram_segment_one_bundles.py b/scripts/scil_tractogram_segment_one_bundles.py
index ae41b209f..060d46144 100755
--- a/scripts/scil_tractogram_segment_one_bundles.py
+++ b/scripts/scil_tractogram_segment_one_bundles.py
@@ -98,7 +98,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, [args.in_tractogram, args.in_transfo])
+    assert_inputs_exist(parser, [args.in_tractogram, args.in_transfo],
+                        args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     wb_file = load_tractogram_with_reference(parser, args, args.in_tractogram)
diff --git a/scripts/scil_tractogram_shuffle.py b/scripts/scil_tractogram_shuffle.py
index 48a8fbbb6..8ffafaaf3 100755
--- a/scripts/scil_tractogram_shuffle.py
+++ b/scripts/scil_tractogram_shuffle.py
@@ -43,7 +43,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
diff --git a/scripts/scil_tractogram_smooth.py b/scripts/scil_tractogram_smooth.py
index 6cc5f07c5..d62e6900d 100755
--- a/scripts/scil_tractogram_smooth.py
+++ b/scripts/scil_tractogram_smooth.py
@@ -79,7 +79,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     assert_outputs_exist(parser, args, args.out_tractogram)
 
     sft = load_tractogram_with_reference(parser, args, args.in_tractogram)
diff --git a/scripts/scil_tractogram_split.py b/scripts/scil_tractogram_split.py
index 5a2a4049e..5eb12a550 100755
--- a/scripts/scil_tractogram_split.py
+++ b/scripts/scil_tractogram_split.py
@@ -84,7 +84,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_tractogram)
+    assert_inputs_exist(parser, args.in_tractogram, args.reference)
     _, out_extension = os.path.splitext(args.in_tractogram)
 
     assert_output_dirs_exist_and_empty(parser, args, [], optional=args.out_dir)
diff --git a/scripts/scil_tractogram_uniformize_endpoints.py b/scripts/scil_tractogram_uniformize_endpoints.py
index f8617b594..9dfc4a04f 100755
--- a/scripts/scil_tractogram_uniformize_endpoints.py
+++ b/scripts/scil_tractogram_uniformize_endpoints.py
@@ -77,7 +77,7 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundle)
+    assert_inputs_exist(parser, args.in_bundle, args.reference)
     assert_outputs_exist(parser, args, args.out_bundle)
 
     sft = load_tractogram_with_reference(parser, args, args.in_bundle)
diff --git a/scripts/scil_visualize_bundles_mosaic.py b/scripts/scil_visualize_bundles_mosaic.py
index 9a6fd5b43..4b10d84e2 100755
--- a/scripts/scil_visualize_bundles_mosaic.py
+++ b/scripts/scil_visualize_bundles_mosaic.py
@@ -175,7 +175,8 @@ def main():
     args = parser.parse_args()
     logging.getLogger().setLevel(logging.getLevelName(args.verbose))
 
-    assert_inputs_exist(parser, args.in_bundles + [args.in_volume])
+    assert_inputs_exist(parser, args.in_bundles + [args.in_volume],
+                        args.reference)
     assert_outputs_exist(parser, args, args.out_image)
     assert_headers_compatible(parser, args.in_bundles + [args.in_volume],
                               reference=args.reference)