RESAMPLING T1


1.  select a new image in the work.log
2.  type "g mrqid" in the unix shell
3.  cd 15_002 (original t1 dir)
4.  mkdir "login name"
5.  cd "login name"
6.  brains
7.  load menu- random image (mrcounter.series.001)
8.  right mouse key- choose resample parameters
	(this turns resampling mode on)
@f1 click above the corpus callosum
	

AXIAL:
9.  f2
10. select a point that best represents the center w/in the ant portion of the 
	interhemispheric fissure (just sup to the corpus callosum)
11. use left mouse key to align crossbars there
12. use right mouse key- select point #1
13. select a point that best represents the center w/in the post portion of the 
	interhemispheric fissure
14. use left mouse key to align crossbars there
15. use right mouse key- select point #2
	keep the points as far apart as possible
16. use right mouse key- align vertical
17. check the alignment 10-15 slices above and below using TOP


CORONAL:
18. type "c"
19. select a point that best represents the center of the interhemispheric 	
	fissure superiorly
20. use left mouse key to align crossbars there
21. use right mouse key- select point #1 
22. select a point that best represents the center of the 3rd ventricle &/or 
	interpeduncular fossa
	(ref: Daniels et al. CRANIAL & SPINAL MRI pg 179)
23. use left mouse key to align crossbars there
24. use right mouse key- select point #2
25. use right mouse key- align vertical
26. check the alignment 10-15 slices forward and back using FRONT

SAGITTAL POST COMM:
27. type "s"
28. f5

make sure that you have a clear mid sag slice at this point; look for:
	a. a clear aquesuct of sylvius
	b. gyrae which are mostly grey matter (exception: occipital lobe)
	c. absence of the cerebellar tonsil
if you're not satisfied w/ the alignment, redo the axial and coronal

29. align crossbars ant to the posterior commissure 
	(ant & sup to cerebral aqueduct of Sylvius)
30. type "c"
31. page back via the slices
32. note the first slice shows the 3rd ventricle filled w/csf
33. a white linear image will appear in the ventricle- this is the post comm 

if you need to make a choice on which slice has the clearest view of the post
	comm, choose the most ant coronal slice

34. align crossbars medial and inf to it
35. type "s"
36. use right mouse key- select point #2
 

SAGITTAL ANT COMM:
37. align crossbars post to the anterior commissure 
	(inf to fornix; ant to mammilary bodies)
	(ref: Daniels et al. CRANIAL & SPINAL MRI pg 103)
38. type "c"
39. page forward via the slices- using f & b ONLY!  
40. DO NOT USE RIGHT OR LEFT OR THE MOUSE!!!
41. once you've seen the entire arc-like structure, choose the best view 
	(midsection and entire arc) 

if you have trouble deciding which is the best view, choose the most post
	coronal slice when picking the ant comm 

42. use up and down to place crossbars sup to the border of the ant comm
43. type "s"
44. use right mouse key- select point #1
45. use right mouse key- align horizontal


CHECKING YOUR WORK:
46. f1
47. make sure each view doesn't look tilted; take a look at mid sag view 
	again; are the temporal lobes close to even on the coronal?

SAVING:
48. save menu- resample parameters
49. type "df ." in the unix shell
50. if result is >30,000 is available then proceed
51. save menu- resample image
52. quit brains
 
You will now have a 10_ACPC subdirectory below the mrqid level directory.
This dir will contain ACPC_mrqid_001--192.pic files and a resample parameters
	file.