Cerebellar Isolation

 

Stripping the volume


Data: High resolution T1-weighted MRI scan.

This is a volume produced by the Montreal Neurological Institute from 27 co-registered scans of the same normal subject.  The voxel size is 1 x 1 x 1 mm.

The scalp, skull, and dura were stripped from the volume using a combination of edge-based, threshold-based and manual approaches. 

The major blood vessels were removed by a method that employed a co-registered proton density scan of the same subject.

 

Defining a cerebellar coordinate system

We chose to transform the original MRI volume into a coordinate system based on cerebellar, rather than cerebral landmarks.

The coordinate system we employ for the cerebellum is based on three anatomical landmarks: the posterior commisure, the obex,  and the apex of the fourth ventricle.  (Although all three points are plotted on the same sagittal slice at right; in fact the apex of the ventricle was located in the adjacent slice.)

We treat the plane defined by these three landmarks as the cerebellar midplane.
The original volume undergoes a rigid-body transformation to satisfy the following conditions:
a) the cerebellar midplane forms the midplane of the volume,
b) the posterior commissure is at the midpoint of the volume, 
c) the line joining the posterior commissure and the obex is vertical.
The resulting resliced volume facilitates examination of cerebellar asymmetry, and is convenient for defining a reproducible approach to isolating the cerebellum from the cerebrum and brainstem.
Coronal slice through the ltip of the lingula: original volume. 

Coronal slice through the tip of the lingula: resliced volume.


 

Isolating the cerebellum

Define landmarks: 
Top of brainstem between superior and inferior colliculi.
Tip of lingula.
Front of nodulus.
Define 4th ventricle mask, with a special label for the roof of the ventricle (defined as portion anterior to the plane containing the tip of the lingula and the front of the nodulus).
Top of brainstem. Plane defining roof of ventricle.

Remove the cerebrum, severing the brainstem in the axial plane containing the landmark.

An initial solution for the cerebral mask is found by warping a template MRI and its associated mask to the target volume. The cerebellar boundary is then refined using a 3D editing tool.
The valid brainstem voxels to cut are all of brainstem in front of the first slice containing cerebellar grey matter and white matter and peduncles back to the plane containing the lingula.

To identify the latter class of voxels we perform the following steps:

1) Use the last brainstem slice in front of the cerebellum to define a candidate mask slice.  Calculate statistics on that slice to define an acceptable intensity range.

2) Project that slice outline forward to the next slice.  Iteratively grow or shrink the outline if the border pixels fall within the designated intensity range. 

3) Perform operator intervention to finalize the mask outline on the current slice.  Calculate new statistics.  Project outline forward.

The animated GIF at right illustrates the process of identifying white matter and peduncles.  At left is the estimated outline from step 2.  At right is the operator-corrected outline.

Restart the animation by clicking "Reload" while holding down the SHIFT key.

 

            Estimated outline                     Operator-corrected outline
"Mill off" the brainstem along a line-of-sight from the front of the brainstem.  The milling operation does not allow undercutting.  That is, it won't cut what it can't see.

An animation of the brainstem removal is stored as a GIF at
right.  It will cycle once. 

Restart the animation by clicking "Reload" while holding down the SHIFT key.

 

Surface extraction

The current surface extraction is a Marching Cubes isosurface extracted from preprocessed MRI data.

The masked cerebellar volume was smoothed with a 5mm boxcar filter and an isosurface threshold was subjectively selected.

Subsequently, the roof of the fourth ventricle was filled with a suprathreshold intensity and the isosurface re-extracted. 

Filling in the fourth ventricle simplifies the 3D surface at the expense of concealing a small section of the grey-matter surface of the nodulus.

The resulting surface has a flat plane which is identified as 
the "plug" that can be cut out of the surface in order to flatten it.  The plug contains no cortical grey matter.  The outline of the plug is plotted at right. 

 

Parcellation of the isolated cerebellum

 

Fissure identiication

The same T1 MRI volume that we used was also used by Schmahmann, Doyon, et al.  in their 1999 article Three-Dimensional MRI Atlas of the Human Cerebellum in Proportional Stereotactic Space .

The authors identified eleven major cerebellar fissures that defined twelve lobes and provided us with the fissure locations within the MRI volume.
 
Vermis lobule 
 Fissure
 Hemisphere lobule
I, II

III

IV

V

VI

VIIAf

VIIAt

VIIB

VIIIA

VIIIB

IX

X
Precentral

Preculminate

Intraculminate

Primary

Superior Posterior

Horizontal

Ansoparamedian

Prepyramidal/Prebiventer

Intrabiventer

Secondary

Posterolateral

 I, II

III

IV

V

VI

Crus I

Crus II

VIIB

VIIIA

VIIIB

IX

X


 
 

Figure 4 of Schmahmann, Doyon, et al.  from Neuroimage 10, 233-260, 1999. 

Lobe Identification

Because we wish to label the flattened cerebellar surface, we created a volume in which each cerebellar voxel was given a lobe label based on the fissure labelling.   The labels were created in the original volume space and then transformed to our cerebellar coordinate system.
 


At right is the resulting cerebellar midplane with the applied labellings.
 
 
 

 
The animated gifs will cycle once.  The initial frame shows Lobe X (nodulus and flocculus).

Restart the animation by clicking "Reload" while holding down the SHIFT key.