Thanks John. I figured it out by trying the batch scripts you provided in an
email.
Another question is: have you tried to segment T1 images acquired with array
coil? SPM5 failed for many cases due to the inhomogeneity. I used FSL to
correct the inhomogeneity, but SPM5 still failed for couple of subjects.
Without the additionally acquired sensitivity map, what would you suggest
for the inhomogeneity correction? (I know this question may be too harsh,
but if anyone else has a good experience, please share)
---------------------------------------------
Ze Wang, Ph. D
Center for functional neuroimaging,
Dept of Neurology,
Medicine school,
University of Pennsylvania
3400 Spruce Stree,
3W Gates building,
Philadelphia, PA 19104
Tel: 215-662-7341
-----Original Message-----
From: John Ashburner [mailto:[log in to unmask]]
Sent: Wednesday, August 27, 2008 6:10 AM
To: zewang; [log in to unmask]
Subject: Re: [SPM] how to use DARTEL for normalizing fMRI con maps?
> To use DARTEL for fMRI group analysis, where should I import the
> individual con files (coregistered to the T1 images)?
Providing your images are registered, then there should be no need to import
your con files. Note that DARTEL hasn't really been evaluated for fMRI
studies. There are likely to be a number of issues relating to how best to
deal with regional expansion and contraction, which are not properly dealt
with by simple warping of the images. I've written about this a number of
times, so I won't go into details here.
> My understanding of
> DARTEL based normalization is that there are two separate registration
> processes, one for grey matter and the other for white matter. How to
> combine these two processes to get a final template?
That is not the case at all. Grey and white matter (and any other classes
that can be well segmented) are registered simultaneously in order to obtain
a consistent estimate of the deformations.
> Another question is: is there a way to use this local template to warp the
> new data sets that are not involved in template generation?
Yes. This is what the "Run DARTEL (existing Templates)" option does.
Best regards,
-John
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