Masking Protocol

Masking example, cerebellum excluded. Coronal and sagittal views shown.

Brain Masking


  1. Go to the directory where your files are located.
  2. To load your brain image, type:
    Display [mnc filename]
    If you have an automated mask (from BET or another automatic masking program), type:
    Display [case#.mnc] -label [automated filename]
    Ex: Display 1112_mean.mnc -label 1112_mean_abet_mask.mnc
  3. On the Display menu, press Color Coding → Gray Scale. Then press Label Opacity. Move your cursor to the shell window and type .15 as your opacity.
  4. Enlarge the mnc window. The intensity bar is on the left side of the screen. Click and drag the lower intensity, usually in green color, to zero. Adjust the upper intensity, usually in blue, to make the image as bright as possible but not to the point of hurting your eyes. The purpose of making the image so bright is so that the meninges and the gray matter can be better separated.
  5. To adjust a subwindow size, click on the center cross and drag. To zoom in or out within a subwindow, move the cursor to that subwindow. Press shift and the middle mouse button at the same time, then move the mouse up for enlargement or down for shrinking. To move the image within a subwindow, press shift and the left mouse button together and drag the image.
  6. Place the cursor into a subwindow, and use "+" and "-" to change the slice number.
  7. To add label, right click and continue pressing when you move the mouse. To erase label, hold on shift and right click the mouse.
  8. To change the brush size, click the space bar in the menu and then choose Segmenting → XY Radius. Move your cursor to the shell window and type the brush size you want.

Useful commands: On your keyboard:

  1. Space + F + T: To erase the label within a label boundary.
  2. Space + F + E: To add the label within a label boundary.
  3. Space + F + B: To temporarily remove the label for better judgments. Press B again to bring back the label.
  4. Space + F + N: To copy the previous slice (posterior) to the next one (anterior).


Starting from the posterior of the brain is easier (that is, you can use command #4 above to speed things up). You can also start from the anterior of the brain, if you prefer. To start from the posterior, click on the most posterior point in the sagittal view. As a general rule of thumb, areas that are extremely bright are nerve tracts, which need to be excluded.

Cerebellum included

Posterior aspect of the brain: In the coronal view, use "+" and "-" to find the starting slice. Click on the region and use the sagittal and axial views to verify.

coronal and sagittal views of brain, posterior aspect
Coronal View Sagittal View

axial view of brain, posterior aspect
Axial View

Medial Aspect of Posterior Brain Regions: Sometimes the sagittal view may be confusing in this region. Use other two views to make your decision. Temporarily removing the label also helps.

sagittal, axial, and coronal views of medial posterior brain regions

Confluence of Sinuses: This area is located where the occipital lobe meets the cerebellum. Exclude this area before the two cerebellar hemispheres meet.

confluence of the sinuses in sagittal and coronal views Sagittal view Coronal view

Once the two cerebellar hemispheres meet, include the medial confluence of sinuses for masking convenience. Do not include the lateral confluence of sinuses.

include the medial confluence of sinuses

Spinal Cord and Medulla: When the spinal cord appears in the coronal view, make the label level with the cerebelli, one of which may disappear earlier than the other in the due to asymmetry.

uneven cerebellar levels

Maintain that level until the natural boundary appears.

uneven cerebellar levels

Cerebellum area: As you move anteriorly, this area can look confusing. Here are some photos that show the cerebellar boundary in three views. The cursor location indicates areas that need attention.

cerebellar boundary examples Sagittal view Coronal view Horizontal view

Trigeminal Nerve: Exclude this structure.

exclude the trigeminal nerve Sagittal view Coronal view

End of Pons: This region contains three nerve tracts that need to be taken out.

oculomotor nerve in coronal and sagittal views
corticobulbar and corticospinal tracts Coronal view Sagittal view

Temporal lobe: The medial and inferior boundary can be confusing, but it is usually faintly visible. Try switching the label on and off and using the other two views to make your decision. The arrows indicate the optic tract and the optic chiasm, which need to be taken out. If the optic tract is barely visible or is not easily accessible in the coronal view, leave it for convenience.

temporal lobe boundaries, sagittal view
temporal lobe boundaries, coronal view

When the temporal lobe begins to shrink in the coronal view, clean up the meninges and nerve tracts on the edges as much as possible but leave those if they are deeply embedded between the temporal lobe and the inferior frontal lobe. Arrows indicate structures that shall not be labeled.

meninges and nerve tracts on edges of temporal lobe are not labeled

When the temporal lobe starts to disappear from the coronal view, use the sagittal view to find the ending point of the temporal lobe.

ending point of temporal lobe

Anterior frontal lobe: The arrows indicate areas that need attention.

anterior frontal lobe

Superior and lateral boundary: Switch the label on and off to better distinguish the gray matter, CSF, and the meninges. Here are some examples; the cursors and arrows indicate areas that need attention.

superior and lateral boundary of frontal lobe


Cerebellum Excluded


In the coronal view, follow the natural boundary of the cerebellum and exclude the confluence of sinuses. Arrows indicate areas that need attention.

cerebellum excluded from mask

The arrows indicate a line that will start to fade. Exclude the brainstem until the line begins fading.

boundary between cerebrum and cerebellum.

Then keep your horizontal cut off line above the cerebellum and above the trochlear IV nerve.

trochlear IV nerve

When the mid line starts to show in the pons region, use the mid line ending point as your cut off boundary.

midline of pons region

From this point on, label areas are the same as those in masks including the cerebellum.