Hello all!

	I have begun to learn spm ,planning to use it for a subject by 
subject analysis, and have been facing a problem concerning 
orientation (I know that the topic has been covered extensively in 
the mailing list but I have not been able to find a specific answer to 
my questions).

	My anatomic and functional images are initially in the following 
orientation (with origin at the center of the volume):

	z:negative on top slice and positive on bottom slice(cerebellum).
	x:negative on the left of the slice and positive on the right of the 
slice.
	y:the back of the brain has positive co-ordinates and the front 
has negative ones.
	ie:the slices are (sort of) in radiologic orientation but with the 
back being were the front should be and if one looks at the sagittal 
view,the brain is 'upside-down'.

	Given the fact I do not want to normalise (at least for now),I 
perform the following reorientation in SPM:<resize x,y,z:-1 and 
crosshair at the AC>:So I am bringing everything (I think),to the 
Talairach orientation.I apply that to the anatomy as well as all the 
functional volumes.
I then :Motion correct and reslice the functional volumes,coregister 
the anatomy to the mean functional image (without reslicing-
target=meanimage,object=t1mri) , segment the anatomy  using the 
results to extract a 3D brain rendering of the subject and smooth 
the functional motion-corrected dataset.(I do not perform slice 
timing correction for now).
	The 3D rendered brain is displayed up-side down (it is difficult 
to say anything about the L-R symmetry),as if no information from 
the *.mat files has been used.The problem persists when I render 
my results on it,though  the 'blobs' seem to be in the correct 
location on the rendered brain structures (given the nature of the 
task performed by the subject).When I display the results on the 
axial slices,the situation persists (the blobs are correctly 
placed,but the anatomy is in the original 'pseudo-radiologic' 
orientation).
	  
My questions are the following:
a:Am I correct in putting everything into Talairach orientation in the 
begginning, since I do not normalise? How does that affect 
segmentation and coregistration? (what do these routines 'assume' 
concerning orientation?,what do I answer to the 'are these MRIs 
spatially normalised?' prompt in 'spm_segment'- I have always 
answered 'no' until now . )
b:Where do my rendering/display problems stem from?Are there 
other routines/functions in spm that are affected?What would be a 
good remedy?   

Thanks!

Charis.


Charidimos Tzagarakis MD
Brain Sciences Center and University of Minnesota.
Address:
Brain Sciences Center (11B)
Minneapolis VA Medical Center
One Veterans Drive
55417 Minneapolis MN
USA
Tel:612-725-2000 ext 1756
email: [log in to unmask] 


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