Turn off thickinthehead by default

Author: Arno Klein

README.rst

@@ -240,7 +240,7 @@ The following steps are performed by Mindboggle (with links to code on GitHub):
 3. Compute volume shape measures for each labeled region:
 
     - volume (`volume_per_brain_region <https://github.com/nipy/mindboggle/blob/master/mindboggle/shapes/volume_shapes.py#L14>`_)
-    - thickness of cortical labels (`thickinthehead <https://github.com/nipy/mindboggle/blob/master/mindboggle/shapes/volume_shapes.py#L132>`_)
+    - thickness of cortical labels (`thickinthehead <https://github.com/nipy/mindboggle/blob/master/mindboggle/shapes/volume_shapes.py#L131>`_, off by default)
 
 4. Compute surface shape measures for every cortical mesh vertex:
 
@@ -346,9 +346,9 @@ The following include outputs from most, but not all, optional arguments.
 
         **volumes_per_ants_label.csv**:  *volume per ANTs label*
 
-        **thickinthehead_per_freesurfer_cortex_label.csv**:  *FS cortex label thickness*
+        **thickinthehead_per_freesurfer_cortex_label.csv**:  *FS cortex label thickness*  **-- UNDER EVALUATION --**
 
-        **thickinthehead_per_ants_cortex_label.csv**:  *ANTs cortex label thickness*
+        **thickinthehead_per_ants_cortex_label.csv**:  *ANTs cortex label thickness*  **-- UNDER EVALUATION --**
 
         [left,right]_cortical_surface /
 

mindboggle/mindboggle

@@ -138,9 +138,9 @@ out_args.add_argument("--no_moments", action='store_true',
                       help="no Zernike moments per surface label or sulcus")
 out_args.add_argument("--no_spectra", action='store_true',
                       help="no Laplace-Beltrami per surface label or sulcus")
-out_args.add_argument("--no_thickness", action='store_true',
-                      help="no volume-based cortical label thicknesses")
 
+adv_args.add_argument("--thickinthehead", action='store_true',
+                      help="volume-based cortical label thicknesses")
 adv_args.add_argument("--fundi", action='store_true',
                       help="extract, measure fundi (under evaluation, SLOW)")
 adv_args.add_argument("--moments",
@@ -259,10 +259,10 @@ if args.no_points:
     do_points = False
 else:
     do_points = True
-if args.no_thickness:
-    do_thickinthehead = False
-else:
+if args.thickinthehead:
     do_thickinthehead = True
+else:
+    do_thickinthehead = False
 
 # Set Laplace-Beltrami spectra:
 if args.no_spectra: