A mask of the cerebellum will be created by subtracting the left and right hemisphere masks from the whole brain mask modifying the results to more exactly trace the cerebellum, and removing the brainstem.

1)  Create a raw cerebellum mask by subtracting the right and left hemisphere masks used for making hemisphere object models from the whole brain mask used to make the lateral surface model.

mincmath -sub #_reslice_mask_1mm_new_blur_label.mnc.gz #_reslice_mask_1mm_L_nocereb.mnc.gz whole-left.mnc
mincmath -sub whole-left.mnc #_reslice_mask_1mm_R_nocereb.mnc.gz whole-left-right.mnc

2)  Display this raw cerebellum mask as a label over the rf-corrected gray scale volume.

Display #_reslice_mr_rf_new.mnc.gz -label whole-left-right.mnc

3)  In the Display window, change the color coding to gray by selecting the "Color Coding" menu (D) from Display's top level and then "Gray Scale" (D).  Change the label opacity to 1 by selecting "Label Opacity" (C) under the Color Coding menu and typing 1 in the UNIX window at the prompt "Enter new label colour opacity".  Change the size of the brush to 5 by selecting the "Segmenting" menu (F) from Display's top level, clicking the "XY Radius" button (F), and typing 5 in the UNIX window at the prompt "Enter xy brush size:".

4)  Starting on the right side of the scan, scroll into the brain using the sagittal view and remove any regions of label that are not near the cerebellum.   Close to midline, there will be more of these areas to remove.

5)  In the Display window, change the label opacity to .3  (D-Color Coding, then C-Label Opacity).  Change the size of the brush to 1 (F-Segmenting, then F-XY Radius).  Adjust the intensity of the scan to a comfortable level.  Magnify the cerebellum in the sagittal view.

6)  Remove the brainstem as described below:

• In the coronal view, begin removal in the most anterior slice where brainstem can be observed. (See Figure 1)
• Continue removal in coronal plane at each slice up to the point where cerebellar grey matter can be observed lateral to the pons. (Figures 2 and 3)
• After identifying the most anterior section where cerebellar grey matter can be observed lateral to the pons, continue removal of the posterior brainstem by excluding only brainstem and pons. (Figure 4)
• No longer exclude the white matter cerebellar peduncles just posterior to the back of the colliculi. (See Figure 5) At this point, just posterior to the colliculi, exclude only the spinal cord inferior to the fourth ventricle by drawing a line connecting the lateral inferior aspect of the fourth ventricle to the lateral superior aspect of the cerebellar grey matter. Drawing this line will exclude the brainstem only. Be sure to draw this line only in sections with CSF between the back of the colliculi and the front of the vermis.
• Once the vermis is clearly visible at the inferior aspect of the fourth ventricle, exclude the brain stem below it but do not exclude the vermis. (See Figure 6)

8)  In the Display window, choose the "File" menu (T), click on "Crop Save Lbls" so it says off, then select  "Save Labels .mnc" (W).

Save as #_reslice_cereb_mask.mnc

The mask will be dilated to include as much cerebrospinal fluid as possible around the cerebellum.

1)  With the mask still up in Display, load the segmented image by selecting "Load File" (F) under the File menu.

Load #_reslice_seg_rf_new.mnc.gz

2)  Set the threshold so only extra CSF is included (not more gray or white matter).  Go to the Segmenting menu (F) and select "Set Threshold" (Y).  Enter a minimum and maximum number that include the signal value assigned to CSF only.  (2.8 and 3.0 for the YALE data).

3)  Be sure the crosshair is within the borders of the mask.  Select "Dilate 3D" (C) under the Segmenting menu.  Enter "0 0" in the UNIX window at the "Enter min and max outside label:" prompt so that Display will dilate into regions correctly labeled with 0 (not in the mask).

4)  Save the dilated mask ( T- File, then W-Save Labels .mnc)

Save as #_reslice_cereb_mask_dilated.mnc
 

Use the mask to create a minc file of the cerebellum.
 

 mincmask #_reslice_mr_rf_new.mnc.gz #_reslice_cereb_mask_dilated.mnc #_reslice_cereb.mnc

Register the cerebellum to the 305 cerebellum so surfaces models can be made and the cerebella of different subjects can be viewed in a common orientation.

1)  Load the average 305 cerebellum and its tag points and the individual's cerebellum in register.

register /loni/edevel/validity/pauls_MASKED_CBLM_icbm_avg_53_t1tal_lin.mnc.gz /loni/edevel/validity/305_cereb_tags.tag #_reslice_cereb.mnc

2)   Set the average cerebellum to gray, and adjust the intensity of the individual cerebellum to a comfortable intensity.

3)  Pick the nine tag points on the individual cerebellum corresponding to the same nine points on the average cerebellum. Be sure to always pick the tag points with the 'record tags' icon located on the left side of the screen.

        The nine tag points are:
        A. Top:  Scroll through the axial view to choose the middle of the most superior piece of the cerebellum.
        B. Bottom (Left and Right):  Scroll through the axial view to choose the middle of the most inferior piece of the
            cerebellum in the left hemisphere, then in the right hemisphere.
        C. Lateral Extremes (Left and Right):  Scroll through the sagittal view to choose the point in the middle of the most lateral
            piece of the cerebellum in left hemisphere, then in the right hemisphere.
        D. Front (Left and Right):  Scroll through the coronal view to choose the point in the middle of the most anterior piece in the
             left and right hemispheres of the cerebellum.
        E. Back (Left and Right):  In the coronal view choose the middle of the most posterior piece in the left hemisphere of the
            cerebellum, then the right hemisphere.

4) Once the tag points have been selected, it is necessary to perform a linear transformation to better place the individual cerebellum in average space. Do so by choosing the lower empty yellow box on the left side of the screen. A menu window will appear. Select '3 Rot'ns & 3 Transl'ns & 3 Scales' and close the menu window. To save the tag points, enter the name of the tag file in the top white box and press 'save tags'.

#_cereb_reslice_to_305.tag

5. Enter the name of the transform file in the second white box and then press the blank yellow box to save.

#_cereb_reslice_to_305.xfm

6)  Use this transformation file to  reorient the individual cerebellum in average 305.

mincresample -short #_reslice_cereb.mnc #_305_cereb.mnc -like /loni/edevel/validity/pauls_MASKED_CBLM_icbm_avg_53_t1tal_lin.mnc.gz -transformation #_cereb_reslice_to_305.xfm
 

Create an object model of the cerebellum.

1)  Determine the threshold to use to create the object model.  Open the resliced 305 cerebellum object in Display.

Display #_305_cereb.mnc
 

2) Go to the "Slice View" menu (S) and choose "Recompute Histogram" (G).  When the histogram appears in the display window, drag the blue line at the top of the bar down to the peak of the histogram.  Drag the green bar from the bottom of the bar to the point at which the histogram starts to ascend.  Calculate the value halfway between these points.

3)  Edit the script create_cereb_objects.csh to include the subject number and thresholds.

nedit ../create_cereb_objects.csh
Change number in quotes after "set subs=" to the subject number.
Put the thresholds in quotes after "set thresh=".  Use 3 thresholds lower than the value calculated in step 2 and two thresholds higher than the value calculated in step 2, each separated by 2 units.  For example, if the threshold found in step 2 was 36, the line would read "set thresh="30 32 34 36 38 40"".

4)  The command goes through the batch queue.  To check on the progress of the processes, select "Loni", then "Utilities", then "System", then "XPS" from the Toolchest.  Click on the long queue and click "Manual Update" in the upper left to monitor the progress.  It should take about 15 minutes to create the objects.

5)  Use Display to pick which threshold will be used.   Display all six objects and the minc that they came from.  Select the lowest threshold in which sulci can be clearly identified by making each surface visible with the others invisible.  Highlight an object on the right side of the Display control panel and select the "Objects" menu (R), then Invisible (Z) or Visible (X) to change which threshold is displayed.  As a further check, the object model can be mapped onto the object by choosing "Scan Object to Vol" (W) from the Ojects Menu.  The line created by the object should follow the border between the gray matter of the cerebellum and the CSF outside it.

Display #_305_cereb_extract_*obj #_305_cereb.mnc

6)  Remove the other object models and gzip the mincs.

gzip *mnc