diff --git a/src/g4synthmorph.py b/src/g4synthmorph.py
index 9b2ee9e..ac1ea6b 100644
--- a/src/g4synthmorph.py
+++ b/src/g4synthmorph.py
@@ -30,7 +30,7 @@ from skimage.metrics import normalized_mutual_information
 import filelock
 import matplotlib.pyplot as plt
 import numpy as np
-import SimpleITK as sitk
+# import SimpleITK as sitk
 
 from mri_synthmorph.synthmorph import registration
 # from synthmorph import registration
@@ -63,40 +63,6 @@ logging.basicConfig(
 logger = logging.getLogger(__name__)
 
 
-# def resize_with_crop_or_pad(image, tx = SIZE_X, ty = SIZE_Y, tz = SIZE_Z):
-def resize_with_pad(image, tx = SIZE_X, ty = SIZE_Y, tz = SIZE_Z):
-    sx, sy, sz = image.GetSize()
-    l = [(tx-sx)//2,
-         (ty-sy)//2,
-         (tz-sz)//2,]
-    u = [tx-sx-l[0],
-         ty-sy-l[1],
-         tz-sz-l[2],
-         ]
-    # print (l, u)
-    return sitk.ConstantPad(image, l, u)
-
-
-def draw_sitk(image, d, post):
-    a = sitk.GetArrayFromImage(image)
-    s = a.shape
-
-    fig, axs = plt.subplots(1, 3)
-    # fig.suptitle('%dx%dx%d'%(s[2], s[1], s[0]))
-    axs.flat[0].imshow(a[s[0]//2,:,:], cmap='gray')
-    axs.flat[1].imshow(a[:,s[1]//2,:], cmap='gray')
-    axs.flat[2].imshow(a[:,:,s[2]//2], cmap='gray')
-    axs.flat[0].axis('off')
-    axs.flat[1].axis('off')
-    axs.flat[2].axis('off')
-    axs.flat[1].invert_yaxis()
-    axs.flat[2].invert_yaxis()
-    plt.tight_layout()
-    os.makedirs(d, exist_ok=True)
-    plt.savefig(os.path.join(d, '%dx%dx%d-%s'%(s[2],s[1],s[0],post)))
-    plt.close()
-    # exit()
-
 def bbox2_3D(img):
 
     r = np.any(img, axis=(1, 2))
@@ -132,6 +98,8 @@ def register(ct0, ct1, moving, out_root):
     logger.info(' '.join((ct0, ct1, moving, str(out_root))))
 
     orig = sf.load_volume(moving)
+
+    base = sf.load_volume(ct0)
     if modality == 'CT':
         clipped = out_root/'clipped.nii.gz'
 
@@ -201,6 +169,11 @@ def register(ct0, ct1, moving, out_root):
     os.environ["FREESURFER_HOME"] = FREESURFER_HOME
     os.environ["XLA_FLAGS"] = '--xla_gpu_cuda_data_dir=%s'% os.environ["CONDA_PREFIX"]
 
+    fill = orig.min()
+    # print(fill)
+    # exit()
+
+
     for m in MODELS:
         default['model'] = m
         default['out_dir'] = out_root/m
@@ -231,16 +204,18 @@ def register(ct0, ct1, moving, out_root):
             out = out_root/('%s.nii.gz'%m)
             if  m in ['affine', 'rigid']:
                 trans = sf.load_affine(default['out_dir']/'tra_1.lta')
-                prop = dict(method='linear', resample=True, fill=0)
-                orig.transform(trans, **prop).save(out)
+                prop = dict(method='linear', resample=True, fill=fill)
+                orig.transform(trans, **prop).resample_like(base, fill=fill).save(out)
                 logger.info('transformed %s'%out)
+                # print(prop)
+                # exit()
             else:
                 # need to resample before transform in warp, too complicated, just copy it
                 # trans1 = default['out_dir']/'tra_1.nii.gz'
                 # trans = sf.load_warp(trans1)
 
-                shutil.copy(default['out_dir']/'out_1.nii.gz', out)
-                logger.info('copied %s'% out)
+                sf.load_volume(default['out_dir']/'out_1.nii.gz').resample_like(base, fill=fill).save(out)
+                logger.info('resampled %s'% out)
 
     with open(out_root/'metric.txt', 'w') as f_metrics:
         for m in MODELS:
@@ -295,7 +270,7 @@ def check(epath):
             if root2.endswith('RT'):
                 modality = 'RT'
                 logger.info('copying %s %s' %(root2, outdir))
-                shutil.copytree(root2, outdir)
+                shutil.copytree(root2, outdir, dirs_exist_ok=True)
                 # exit()
                 continue 
             skip = (root2==root) or ('RT' in root2.split('/'))