Dear Chikashi,
|Now I have a problem in normalisation.
|I realigned the fM* images specifying Coregister&reslice => sinc
|interpolation => mean image only. It was successful. I got rf*.imgs and
|mean*.img.
|Then I coregistered sM* structural image, with options as Coregister
|only => target=sM*img(T1) => object=mean*.img(T2). Now this was successful,
|I got rmean*.img.
I think that the problem you are having is actually in the coregistration,
which is then leading to problems normalising. Here's what I think is
happening.
You have realigned all the functional images together, so they are then in
the same anatomical space. The structural image is initially in a
different anatomical space. However you then coregister the mean
functional to the structural (rather than the other way around) thus
moving the rmean*.img into the anatomical space of the structural. As this
space happens to be offset, when you normalise the s*.img you generate
paramters that would correctly normalise the rmean*.img, but NOT the
rfM*.img's, which are in a different anatomical space.
The solution is to coregister the structural to the mean functionals (i.e.
target = T2, object = T1) creating a rsM.img that you then normalise as
you have done. This puts all the T2*, T1 and meanT2* images
in the same anatomical space. Alternatively just normalise
the mean*.img directly to the EPI template, bypassing the structural
altogether.
Good luck!
best wishes,
Geraint
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Dr. Geraint Rees
Wellcome Advanced Fellow Lecturer
California Institute of Technology Institute of Neurology
Division of Biology 139-74 University College London
Pasadena 12 Queen Square
California 91125 London WC1N 3BG
voice (626) 395-2880 voice (171) 833-7472
fax (626) 796-8876 fax (171) 813-1420
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