antspymm 1.3.7__py3-none-any.whl → 1.3.9__py3-none-any.whl

antspymm/mm.py

@@ -5017,8 +5017,6 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   nmdf_wide = antspyt1w.merge_hierarchical_csvs_to_wide_format(
               {'NM' : nmdf},
               col_names = ['Mean'] )
-  if verbose:
-      print( "nm done" )
 
   rr_mask = ants.mask_image( labels2nm, labels2nm, [33,34] , binarize=True )
   sn_mask = ants.mask_image( labels2nm, labels2nm, [7,9,23,25] , binarize=True )
@@ -5028,7 +5026,8 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   rravg = nm_avg_cropped[ rr_mask == 1].mean()
   snstd = nm_avg_cropped[ sn_mask == 1].std()
   rrstd = nm_avg_cropped[ rr_mask == 1].std()
-  snvol = np.prod( ants.get_spacing(sn_mask) ) * sn_mask.sum()
+  vol_element = np.prod( ants.get_spacing(sn_mask) )
+  snvol = vol_element * sn_mask.sum()
 
   # get the mean voxel position of the SN
   if snvol > 0:
@@ -5037,7 +5036,34 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
   else:
       sn_z = math.nan
 
-  nm_evr = antspyt1w.patch_eigenvalue_ratio( nm_avg, 512, [6,6,6], evdepth = 0.9, mask=cropper2nm )
+  nm_evr = 0.0
+  if cropper2nm.sum() > 0:
+    nm_evr = antspyt1w.patch_eigenvalue_ratio( nm_avg, 512, [6,6,6], 
+        evdepth = 0.9, mask=cropper2nm )
+
+  simg = ants.smooth_image( nm_avg_cropped, np.min(ants.get_spacing(nm_avg_cropped)) )
+  k = 2.0
+  rrthresh = (rravg + k * rrstd)
+  nmabovekthresh_mask = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
+  snvolabovethresh = vol_element * nmabovekthresh_mask.sum()
+  snintmeanabovethresh = float( ( simg * nmabovekthresh_mask ).mean() )
+  snintsumabovethresh = float( ( simg * nmabovekthresh_mask ).sum() )
+
+  k = 3.0
+  rrthresh = (rravg + k * rrstd)
+  nmabovekthresh_mask3 = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
+  snvolabovethresh3 = vol_element * nmabovekthresh_mask3.sum()
+
+  k = 4.0
+  rrthresh = (rravg + k * rrstd)
+  nmabovekthresh_mask4 = sn_mask * ants.threshold_image( simg, rrthresh, math.inf)
+  snvolabovethresh4 = vol_element * nmabovekthresh_mask4.sum()
+  
+  if verbose:
+    print( "nm vol @2std above rrmean: " + str( snvolabovethresh ) )
+    print( "nm intmean @2std above rrmean: " + str( snintmeanabovethresh ) )
+    print( "nm intsum @2std above rrmean: " + str( snintsumabovethresh ) )
+    print( "nm done" )
 
   return{
       'NM_avg' : nm_avg,
@@ -5053,6 +5079,11 @@ def neuromelanin( list_nm_images, t1, t1_head, t1lab, brain_stem_dilation=8,
       'NM_avg_substantianigra' : snavg,
       'NM_std_substantianigra' : snstd,
       'NM_volume_substantianigra' : snvol,
+      'NM_volume_substantianigra_2std' : snvolabovethresh,
+      'NM_intmean_substantianigra_2std' : snintmeanabovethresh,
+      'NM_intsum_substantianigra_2std' : snintsumabovethresh,
+      'NM_volume_substantianigra_3std' : snvolabovethresh3,
+      'NM_volume_substantianigra_4std' : snvolabovethresh4,
       'NM_avg_refregion' : rravg,
       'NM_std_refregion' : rrstd,
       'NM_min' : nm_avg_cropped.min(),

{antspymm-1.3.7.dist-info → antspymm-1.3.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: antspymm
-Version: 1.3.7
+Version: 1.3.9
 Summary: multi-channel/time-series medical image processing with antspyx
 Author-email: "Avants, Gosselin, Tustison, Reardon" <stnava@gmail.com>
 License: Apache 2.0

antspymm-1.3.9.dist-info/RECORD

@@ -0,0 +1,7 @@
+antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
+antspymm/mm.py,sha256=m4l1VoltZnGqiKzLg1kOGRwx3INA87DkPZHJ4sU7cxE,481240
+antspymm-1.3.9.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+antspymm-1.3.9.dist-info/METADATA,sha256=Ceg-uz1GUm1QPikt40iS9MkbF_7xJVgr4s-_1svpyr8,14866
+antspymm-1.3.9.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+antspymm-1.3.9.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
+antspymm-1.3.9.dist-info/RECORD,,

antspymm-1.3.7.dist-info/RECORD

@@ -1,7 +0,0 @@
-antspymm/__init__.py,sha256=1fHqufHndrkJwz473av8qOf5-1xm5r-aKHuMAETGIiE,4462
-antspymm/mm.py,sha256=iQkwK-YcD6cYQhtIYKWhOW5vqVtGWBbzH6pfSqq_oN0,479836
-antspymm-1.3.7.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-antspymm-1.3.7.dist-info/METADATA,sha256=SFxaPK9kMEgxJMx_CITvyWR3mWOzntIvKLHE1QKojRk,14866
-antspymm-1.3.7.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-antspymm-1.3.7.dist-info/top_level.txt,sha256=iyD1sRhCKzfwKRJLq5ZUeV9xsv1cGQl8Ejp6QwXM1Zg,9
-antspymm-1.3.7.dist-info/RECORD,,