Dear
all,
I wish to
normalise my T1 (to the MNI template) and use the obtained parameters for
normalisation of the EPIs, as is fairly standard. In order to 'aid' the
normalisation, I want to set the orientation to the AC manually in the Display
function, but I have a few questions about this, that keep getting me
confused:
- Does it matter if
I set the orientation on the T1 before or after the coregistration of
the T1 to my mean_EPI?
- If I draw a lesion
mask in MRICro, to be used in cost function masking, should I do this on the
coregistered T1, and should I do this on the T1 before or after having set the
orientation manually in SPM?
Conceptually, my
problem is that I would assume that if you change information on the T1 (e.g.
its orientation), you cannot use the parameters obtained from normalising that
changed T1 to normalise EPIs that were not changed in the same way. Or does
setting the orientation not change the position of my T1 relative to the
EPIs? Likewise, if I draw a lesion map on a 'raw' T1 and then later change
the orientation settings of that T1, or coregister it to other images, I would
assume that I cannot use that unaltered lesion map to overlay it on
the altered T1 during cost function masked normalisation ...
Any enlightenment is
much appreciated! Thanks,
Dirk
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Dirk-Bart den Ouden, Northwestern University
Aphasia & Neurolinguistics Research Laboratory
Dept. of
Communication Sciences & Disorders
2240 Campus
Drive, Evanston IL
60208-3066
Phone (lab):
1-847-467-7591
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