diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 6ed038f1a15edbe4acd090b7bc4af55f4778d852..259b91fdf41bc84490a6ecf28344d09ce3ce8c19 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -483,8 +483,8 @@ class AtlasDescription(object):
 
         self.atlasID   = atlasID
         self.specPath  = op.abspath(filename)
-        self.name      = header.find('name').text
-        self.atlasType = header.find('type').text.lower()
+        self.name      = header.find('name').text.strip()
+        self.atlasType = header.find('type').text.strip().lower()
 
         # Spelling error in some of the atlas.xml files.
         if self.atlasType == 'probabalistic':
@@ -501,8 +501,8 @@ class AtlasDescription(object):
         for image in images:
 
             # Every image must also have a summary image
-            imagefile        = image.find('imagefile')       .text
-            summaryimagefile = image.find('summaryimagefile').text
+            imagefile        = image.find('imagefile')       .text.strip()
+            summaryimagefile = image.find('summaryimagefile').text.strip()
 
             # Assuming that the path
             # names begin with a slash
@@ -533,7 +533,7 @@ class AtlasDescription(object):
 
         for i, label in enumerate(labels):
 
-            name  = label.text
+            name  = label.text.strip()
             index = int(  label.attrib['index'])
             x     = float(label.attrib['x'])
             y     = float(label.attrib['y'])
diff --git a/fsl/scripts/atlasq.py b/fsl/scripts/atlasq.py
index 10acf8ff24c6548f51a7cdb96e4e8dcd43132d6c..486e2c02a719cb93cfe5729285d24e743565a190 100644
--- a/fsl/scripts/atlasq.py
+++ b/fsl/scripts/atlasq.py
@@ -171,8 +171,8 @@ def queryLongOutput(atlas, sources, types, allLabels, allProps):
         label = labels[0]
         name  = names[ 0]
 
-        if label is None:
-            label = np.nan
+        if label is None: label = np.nan
+        else:             label = int(label)
 
         fields = ['name', 'index']
         values = [name, label]
@@ -304,7 +304,7 @@ def ohi(namespace):
                 props, labels = zip(*reversed(sorted(zip(props, labels))))
 
             for label, prop in zip(labels, props):
-                label = atlasDesc.labels[label].name
+                label = atlasDesc.labels[int(label)].name
                 labelStrs.append('{:d}% {}'.format(int(round(prop)), label))
 
             if len(labelStrs) == 0: labels = 'No label found!'
@@ -331,7 +331,7 @@ def labelNames(atlas, labels):
 
     for l in labels:
         if l is None: names.append('No label')
-        else:         names.append(atlas.desc.labels[l].name)
+        else:         names.append(atlas.desc.labels[int(l)].name)
 
     return names