Dear David:
I think one problem you are having is that you don't normalize the gray and
white matter separately and then apply both normalizations back to the
original image, you just use the gray.
So here are the basic steps:
1) Segment the T1 volume (it is not normalized at this point)
This will create gray, white and csf images.
2) Normalize the gray matter segment to the gray matter template. This is
in spm_directory/apriori/gray.mnc
3) Apply gray matter normalization parameters back to original image (use
the *seg1_sn.mat file as the normalization parameter file).
4) Segment the now normalized T1 volume
This will create normalized gray, white and csf images
There's also the issue of jacobian modulation which you can specify by the
normalization defaults, creating your own template, etc.
Fortunately there are some very nice tools out there for setting this up
and doing the work. See Christian Gaser's page
http://dbm.neuro.uni-jena.de/vbm.html which provides several scripts that
are based on scripts and emails from John Ashburner.
Regards,
Darren
At 04:08 PM 1/14/2005, Kareken, David A. wrote:
>I am trying to find the answer to this very question, as posed a year ago in:
><http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0307&L=spm&P=R15932&I=-1>http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0307&L=spm&P=R15932&I=-1
>
>Specifically, in the optimized VBM approach (using SPM2), I do not
>understand exactly how one re-applies the normalization parameters from
>the separate gray and white matter normalizations to the original native
>whole brain image. That is, if I understand the process correctly, one
>needs to apply two separate sets of normalization parameters (one for
>gray, one for white) to one whole brain image, and I don't understand how
>to go about doing that (SPM provides for applying only one mat file to a
>given image, yes?). Am I misunderstanding the process?
>
>Thanks for any help!
>
>David A. Kareken, Ph.D., ABPP/ABCN
>Board Certified Neuropsychologist
>Associate Professor & Director of Neuropsychology
>Department of Neurology (RI-1773)
>Indiana University School of Medicine
>Indianapolis, IN 46202
>Tel: 317 274-7327
>Fax: 317 274-1337
>
>
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Darren R. Gitelman, M.D.
Cognitive Neurology and Alzheimer¹s Disease Center
Northwestern Univ., 320 E. Superior St., Searle 11-470, Chicago, IL 60611
Voice: (312) 908-9023 Fax: (312) 908-8789
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