diff --git a/brainiak/utils/fmrisim.py b/brainiak/utils/fmrisim.py
index 41c5d73dd..05838abf1 100644
--- a/brainiak/utils/fmrisim.py
+++ b/brainiak/utils/fmrisim.py
@@ -523,10 +523,6 @@ def generate_stimfunction(onsets,
         # Store the weights
         stimfunction[onset_idx:offset_idx, 0] = [weights[onset_counter]]
 
-    # Shorten the data if it's too long
-    if stimfunction.shape[0] > total_time * temporal_resolution:
-        stimfunction = stimfunction[0:int(total_time * temporal_resolution), 0]
-
     return stimfunction
 
 
diff --git a/brainiak/utils/utils.py b/brainiak/utils/utils.py
index 1e7084266..56119e02a 100644
--- a/brainiak/utils/utils.py
+++ b/brainiak/utils/utils.py
@@ -427,10 +427,10 @@ def gen_design(stimtime_files, scan_duration, TR, style='FSL',
     n_C = len(stimtime_files)  # number of conditions
     n_S = np.size(scan_duration)  # number of scans
     if n_S > 1:
-        design = [np.empty([int(np.floor(duration / TR)), n_C])
+        design = [np.empty([int(np.round(duration / TR)), n_C])
                   for duration in scan_duration]
     else:
-        design = [np.empty([int(np.floor(scan_duration / TR)), n_C])]
+        design = [np.empty([int(np.round(scan_duration / TR)), n_C])]
     scan_onoff = np.insert(np.cumsum(scan_duration), 0, 0)
     if style == 'FSL':
         design_info = _read_stimtime_FSL(stimtime_files, n_C, n_S, scan_onoff)
@@ -445,21 +445,24 @@ def gen_design(stimtime_files, scan_duration, TR, style='FSL',
     # generate design matrix
     for i_s in range(n_S):
         for i_c in range(n_C):
-            stimfunction = generate_stimfunction(
-                onsets=design_info[i_s][i_c]['onset'],
-                event_durations=design_info[i_s][i_c]['duration'],
-                total_time=scan_duration[i_s],
-                weights=design_info[i_s][i_c]['weight'],
-                temporal_resolution=1.0/temp_res)
-            hrf = _double_gamma_hrf(response_delay=response_delay,
-                                    undershoot_delay=undershoot_delay,
-                                    response_dispersion=response_disp,
-                                    undershoot_dispersion=undershoot_disp,
-                                    undershoot_scale=undershoot_scale,
-                                    temporal_resolution=1.0/temp_res)
-            design[i_s][:, i_c] = convolve_hrf(
-                stimfunction, TR, hrf_type=hrf, scale_function=0,
-                temporal_resolution=1.0 / temp_res).transpose() * temp_res
+            if len(design_info[i_s][i_c]['onset']) > 0:
+                stimfunction = generate_stimfunction(
+                    onsets=design_info[i_s][i_c]['onset'],
+                    event_durations=design_info[i_s][i_c]['duration'],
+                    total_time=scan_duration[i_s],
+                    weights=design_info[i_s][i_c]['weight'],
+                    temporal_resolution=1.0/temp_res)
+                hrf = _double_gamma_hrf(response_delay=response_delay,
+                                        undershoot_delay=undershoot_delay,
+                                        response_dispersion=response_disp,
+                                        undershoot_dispersion=undershoot_disp,
+                                        undershoot_scale=undershoot_scale,
+                                        temporal_resolution=1.0/temp_res)
+                design[i_s][:, i_c] = convolve_hrf(
+                    stimfunction, TR, hrf_type=hrf, scale_function=False,
+                    temporal_resolution=1.0 / temp_res).transpose() * temp_res
+            else:
+                design[i_s][:, i_c] = 0.0
             # We multiply the resulting design matrix with
             # the temporal resolution to normalize it.
             # We do not use the internal normalization
diff --git a/tests/utils/example_stimtime_2_AFNI.txt b/tests/utils/example_stimtime_2_AFNI.txt
new file mode 100644
index 000000000..39d03d9ee
--- /dev/null
+++ b/tests/utils/example_stimtime_2_AFNI.txt
@@ -0,0 +1 @@
+-10.0
diff --git a/tests/utils/test_utils.py b/tests/utils/test_utils.py
index 820b648e8..1348790db 100644
--- a/tests/utils/test_utils.py
+++ b/tests/utils/test_utils.py
@@ -101,7 +101,8 @@ def test_gen_design():
     import os.path
     files = {'FSL1': 'example_stimtime_1_FSL.txt',
              'FSL2': 'example_stimtime_2_FSL.txt',
-             'AFNI1': 'example_stimtime_1_AFNI.txt'}
+             'AFNI1': 'example_stimtime_1_AFNI.txt',
+             'AFNI2': 'example_stimtime_2_AFNI.txt'}
     for key in files.keys():
         files[key] = os.path.join(os.path.dirname(__file__), files[key])
     design1 = gen_design(stimtime_files=files['FSL1'], scan_duration=[48, 20],
@@ -130,6 +131,11 @@ def test_gen_design():
                          scan_duration=[48, 20], TR=2, style='AFNI')
     assert np.all(np.isclose(design1, design6)), (
         'design matrices generated from AFNI style and FSL style do not match')
+    design7 = gen_design(stimtime_files=[files['AFNI2']],
+                         scan_duration=[48], TR=2, style='AFNI')
+    assert np.all(design7 == 0.0), (
+        'A negative stimulus onset of AFNI style should result in an all-zero'
+        + ' design matrix')
 
 
 def test_center_mass_exp():