PICKING TALAIRACH PARAMETERS


1.  select a resampled image in the work.log or mrqid of interest
2.  type full path to mrqid   (ex:"/usr/anu/MR/pid/mrqid")
3.  ls
4.  cd 10 acpc
5.  ls (to check if talairach has already been done)
6.  mkdir "login name"
7.  cd "login name"
8.  brains
9.  load image (load the acpc_$mrqid_001.pic image one dir above)
10. type "prompt_talairach" in the unix shell

FRONT BOUNDRY:
11. set crossbars slightly post the most ant point of the axial grey matter
	(do this from sagittal view at side slice 127)
12. page f until the grey matter disappears
13. select the point at which the grey matter has completely disappeared
	in the CORONAL plane
	consult the other views, also
14. list the # in front box as the front boundary in the unix shell prompt


BACK BOUNDARY:
15. set crossbars slightly ant to the most post point of the axial grey matter  
	(do this from sagittal view at side slice 127)
16. page b until the grey matter disappears
17. select the point at which the grey matter has completely disappeared
	in the CORONAL plane
	consult the other views, also
18. list the # in the front box as the back boundary in the unix shell prompt


ANATOMICAL LEFT BOUNDARY:
19. set crossbars medial to the far anatomical left of the axial view
20. page l until you can no longer see grey matter 
	in the SAGITTAL plane
	consult the other views
21. list the # in the side box as the anatomical left in the unix shell prompt


ANATOMICAL RIGHT BOUNDARY:
22. set crossbars medial to the far anatomical right of the axial view
	(recall: anatomical right is on the left of the screen)
23. page r until you no longer see grey matter
	in the SAGITTAL plane
	consult the other views
24. list the # in the side box as the anatomical right in the unix shell prompt


ANATOMICAL TOP BOUNDARY:
25. set crossbars just inf to the most sup portion of the grey matter on 
	the sagittal view
26. be careful of the membranes! 
27. select the first point where the grey matter disappears 
	in the AXIAL plane (regardless of whether the membrane is present)
28. list the # in the top box as the top boundary in the unix shell prompt  


ANATOMICAL BOTTOM BOUNDARY:
29. set crossbars just sup to the most inf portion of the temporal lobe
	using either the sagittal or the coronal views
30. select the first point where the grey matter disappears
	in the AXIAL plane (look just inf to the eyeballs)
31. list the # in the top box as the bottom boundary in unix shell prompt


CHECKING YOUR WORK:
32. load menu: Talairach bounds
33. make sure the entire brain is within the boundaries