Hi John,
Thanks for pointing out the lines 311, 160, and 163 (SPM5).
I could understand the effects of lines 160 and 163 (global scaling).
I have two more questions on line 311 (the expression s = T((s1+1):end):
1) what are these "4" scaling factors? Why not just one?
2) how to use these factors? Multiply or divide them to the source to make
it match to the target, or ...?
Thanks for your patience.
James Yu
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: Monday, February 06, 2006 3:06 AM
To: James Yu; [log in to unmask]
Subject: Re: [SPM] Scaling in normalization
> I read that when SPM2 does spatial normalization, it also searches for
> optimal pixel value scaling factor. Is there anyway to know what this
> final value is once the normalization is done?
There are actually 4 scaling factors that are supposed to model linear
intensity variability over the volume. You can get these from
spm_normalise.m at around line 311 by including e.g:
s = T((s1+1):end)
and somehow saving the value of s. Note also that you'll need to include
the
scaling effects from around lines 160 and 163, which scales the intensities
to be within a more reasonable range.
Best regards,
-John
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