The images released with SPM2 are in MINC format, so I'm not sure how
you are comparing them with the aal volume in MRIcro (does MRIcro read
MINC?).  The orientation information about the ROI_MNI_V4.img is not
actually saved in its header or any .mat file.  Instead, I believe the
authors hard-coded the transformation from voxels to MNI space within
the code of the toolbox.  Therefore, if you plan to use the volume for
anything other than use with the toolbox, you'll need to fix the headers
etc so the orientation and position information is correct.

I would guess that MRIcro aligns volumes voxel-for voxel, whereas SPM
makes use of position and orientation information in the headers (or mat
files).  You may need to check with Chris R for a more definitive
answer.

Best regards,
-John

-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
On Behalf Of Markus Burgmer
Sent: Thursday, November 16, 2006 12:29 PM
To: [log in to unmask]
Subject: [SPM] aal template orientation in spm2

dear list (i hope i am using the correct list)

i am having problems with the orientation of the aal template in spm2 
(transverse slice) and could not find anything in the list archives (but
i 
have to admit, this is my first visit).
for example the resulting activation in spm2 is -24 -26 66. the aal
toolbox 
gives me the anatomical localisation of "left pre-, postcentral gyrus", 
which looks pretty correct for me, esp. the side of activation. i like
to 
check my result in spm2 with overlaying the result onto the aal
template. 
what i see is that the activation appears on the right side of the
image, 
which never occured strange to me before, because i thought this to be a

anatomical/neurological view problem.
viewing the same aal template in mricro gives me a big suprise. while
the 
aal template in spm and in mricro has the same orientation, the above 
mentioned activation is switched in mricro because it now refers to the 
left side of the template. 
does anybody knows the problem?

i hope someone has an idea.

thanks a lot

markus burgmer