FIX: avoid including pixdim[0]/qfac in voxel volume calculation

Author: jhuguetn

pyxnat/core/derivatives/bamos.py

@@ -29,7 +29,7 @@ def volume(self):
     f = list(self.files('CorrectLesion_*nii.gz'))[0]
     f.get(fp)
     d = nib.load(fp)
-    size = np.prod(d.header['pixdim'].tolist()[:4])
+    size = np.prod(d.header['pixdim'].tolist()[1:4])
     n = np.array(d.dataobj)
     v = np.sum(n[n >= 0.5]) * size
     os.remove(fp)
@@ -66,7 +66,7 @@ def _download_data_(self):
         f = list(self.files('CorrectLesion_*nii.gz'))[0]
         f.get(fp)
         d = nib.load(fp)
-        size = np.prod(d.header['pixdim'].tolist()[:4])
+        size = np.prod(d.header['pixdim'].tolist()[1:4])
         les = np.array(d.dataobj)
 
         f = list(self.files('Layers_*.nii.gz'))[0]

pyxnat/core/derivatives/basil.py

@@ -17,7 +17,7 @@ def volumes(self):
         f = self.files('*{}*'.format(kls))[0]
         f.get(fp)
         d = nib.load(fp)
-        size = np.prod(d.header['pixdim'].tolist()[:4])
+        size = np.prod(d.header['pixdim'].tolist()[1:4])
         v = np.sum(d.dataobj) * size
         vols.append((kls, v))
 

pyxnat/core/derivatives/cat12.py

@@ -16,7 +16,7 @@ def volumes(self):
         f = [each for each in self.files() if each.id().startswith(kls)][0]
         f.get(fp)
         d = nib.load(fp)
-        size = np.prod(d.header['pixdim'].tolist()[:4])
+        size = np.prod(d.header['pixdim'].tolist()[1:4])
         v = np.sum(d.dataobj) * size
         vols.append((kls, v))
 

pyxnat/core/derivatives/fsl_anat.py

@@ -41,7 +41,7 @@ def subcortical_volumes(self):
         f.get(fp)
         img = nib.load(fp)
         data = np.asarray(img.dataobj)
-        voxel_size = np.prod(img.header['pixdim'].tolist()[:4])
+        voxel_size = np.prod(img.header['pixdim'].tolist()[1:4])
 
         for roi, label in labels.items():
             volume = np.count_nonzero(data == label) * voxel_size

pyxnat/core/derivatives/spm12.py

@@ -16,7 +16,7 @@ def volumes(self):
         f = [each for each in self.files() if each.id().startswith(kls)][0]
         f.get(fp)
         d = nib.load(fp)
-        size = np.prod(d.header['pixdim'].tolist()[:4])
+        size = np.prod(d.header['pixdim'].tolist()[1:4])
         v = np.sum(d.dataobj) * size
         vols.append((kls, v))