PICKING VB,BG,BW TRACES


1.  open the work.log using control+alt+o (mrquid of interest)
2.  find a case that needs vb, bg, bw traces
3.  type g and paste the mrqid in the unix shell
4.  ls
5.  select the 10 acpc dir (remember to avoid problem drives)
6.  ls
7.  check to see if there's already a mrqid_stereo.img in the 10acpc dir

we would also like to see if anyone has traced the rois yet- to do this type 
	"ls */* [bs][gwf].zroi"
it will either show you the traces of complain that there are no matches found

8.  if not, proceed
9.  mkdir login name
10. cd login name
11. brains
12. load menu: t1,t2 (10 acpc_mrqid_001.pic,mrqid_f2_fit.img)
13. select the structure you're about to trace
 	ie: r_vb, l_vb, bg, bw

WHEN TRACING BLOOD:
14. select coronal slice 30
15. zoom to f11
16. look in the concave area on the ant right
17. in t2 we're looking for dk black squares (0-15)
18. in t1 we're looking for various shades of grey; NOT WHITE!!! (55-75)
	never pick voxels w/greater than 80 pixel intensity on t1)	
19. trace squares that meet both criteria on slice 30 through 40
	toggle b/tn images using insert "0" key
20. after each blood tracing, move forward
21. repeat steps 16-20 for ant left

sometimes on smaller brains you will have a better section through the dural
	venous sinuses if you trace coronal slices 35-50

rule of thumb for blood:  it's better NOT to include borderline voxels
	more it not better in this case b/c these voxels enter right into 
	the discriminate analysis 


WHEN TRACING BASAL GREY:
22. zoom out to f3
23. return to sagittal view
24. place crossbars in front of cerebral aqueduct of sylvius
25. change to coronal
26. staring at the back of the thalamus, page forward until the thalamus 
	merges with the brainstem 
	(start @ front 80 until the 3rd ventricle is apparent)
27. select the structure you're tracing: bg
28. trace 15-20 circles of grey matter w/in the thalamus 																
	(stay away from the edges; avoid white matter)
29. trace every other side- right then left then right

bg traces are usually traced on coronal slices 80-95; these traces are only 
	used to determine a threshold for measuring the subcortical box; b/c
	they are not used in discriminant analysis it is not as important to 
	be so maticulate 


WHEN TRACING BASAL WHITE:
30. start on the last slice you finished for bg
31. change selection to bw
32. repeat the tracing pattern for bw
33. choose white matter in lower internal capsule  
	(stay away from the edges; avoid grey matter)
34. again trace every other side- l,r,l


35. quit brains