TRIMMING NON_CRAN ROI'S

	
01. select the image on which to trim non_cran roi's 
02. type "g mrqid" in the unix shell
03. cd to the 10_ACPC dir
04. type "ls"
05. check to see that "mrqid_stereo.img" exists in that 10_ACPC dir
06. begin checking the user directories ???????????? in search of the
	non_cran.zroi's
 	ie: cd to the user (login name) dir and type ls
07. if the non_cran.zroi's are in someone else's dir, you must copy 
	them to your user dir
08. to copy non_cran.zroi's:
	a. in the 10_ACPC dir type "mkdir login name"
	b. cd to that new dir  (ie: cd helen)
	c. type "cp full path to the 10_ACPC/tracer/*non_cran* full path
		to the 10_ACPC/login name
	d. now these traces are in your directory
	e. e-mail the original tracer instructing them to remove the 
		traces from their directory


09. start brains
10. load menu- image
11. load stereo.img
12. load menu- image
13. load t1 image
14. load menu- image
15. load pd/t2 image 
16. zoom in @ f2 on the coronal
17. set front# to "1"
18. use your right mouse button to set foreground roi to non_cran
	(this will cause the trace to turn red)

Note: This step is different from previos steps in that it does not follow
a series of step by step instructions.  Instead it uses general rules of 
thumb that allow us to edit our non_cran roi's.


19. page forward until you see brain (& surface csf)
20. you should see the hemispheres which are small at first
	as you go forward, they enlarge and the cerebellum emerges
21. the net has already traced the brain, the point here is to edit any
	gross mistakes (>4 pixels)
22. if an area is questionable as to whether or not it is brain or surface 
	csf, page forward to see whether it develops into brain or not; be 
	sure to use the other modalities for clarification
23. if you see an area that either mistakenly excludes brain and/or surface 
	csf or includes non-brain material, edit it
24. to edit:
	a. use the right mouse key; choose edit foreground roi
	b. use the left mouse key to click in close proximity to the left 
		of the area you want to edit
	c. use the left mouse key to click w/in the area to be editted
	d. use the left mouse key to click in close proximity to the right 
		of the area you want to edit 
	e. hold the left mouse key down and retrace the editted area from
		right to left
	f. be sure to edit the smallest area of the original trace as possible!!!

Note: all tracing is done on the stereo image; the other modalities are only
used to aid in the idnetification of certain areas and structures

25. when the vertebral artery comes into view, align the crosshares in the
	middle of the most superior artery (ref: Yuh et al. MRI of Head & 
	Neck Anatomy pg 145-146)
26. as you page forward, the artery will move; 	be sure to move the cross-
	hares, keeping them in the middle of the artery as it moves
27. the horizontal line from the crosshares is now used as the cut off point
	for the inferior boarder of our trace
28. exclude brain stem and cord below the horizontal cross-hare guideline
29. include the cisterna magna in the traces
	 (ref: Yuh et al. MRI of Head & Neck Anatomy pg 122)   
30. once you see the permanent seperation of white matter in the cord,
	discontinue using the horizontal guide line as the inferior boarder
	(ref: Yuh et al. MRI of Head & Neck Anatomy pg 115)
31. the new inferior boarder should include only the pons, medulla oblongata, 
	and surrounding csf
32. when editting the superior and lateral boarders of the brain, be sure 
	dura mater is excluded from this trace
33. eventually the pons will appear to break away from the rest of the
	brain (ref: Yuh et al. MRI of Head & Neck Anatomy pg 110)    
34. the inferior boarder of the trace should hug the temporal lobes, removing
	the pools of csf, and boardering the inferior of the sphenoid sinus
35. don't allow the trace to dip down into the eyeballs
36. make sure every slice of brain and surface csf is included in the trace

37. quit brains