Hi David:
We have seen the exact same thing, kind of like high vacuum was applied to
the top of the head. Actually worse than the fact that this occurs, is that
it occurs differently for each subject so group normalization sucks. This
seems to be due to signal inhomogeneity from the coil, the sequence or
whatever. We had the same problem with the Transmit/Receive and the
8-channel head coil. Our physicist hasn't had much luck with adjusting the
MPRAGE sequence per se (but see below) and we were unable to implement
satisfactorily the MDEFT sequence written up by Ralf Deichmann. By the way
even though the MPRAGE images don't "look" that bad, if you do a bias
correction on one of the bad volumes and then plot the bias field the
region requiring warping becomes obvious.
Anyway I've tried a number of techniques to fix this. As you note
segmenting the brain and normalizing the gray matter segment to the apriori
gray matter image can help, but doesn't always solve the problem because
the gray matter segmentation is also affected by the inhomogeneity. So the
gray matter at the top of the head is subtly deficient and then normalizes
poorly.
I spent one weekend coming up with a complicated sequence of steps to
minimize the distortions, which required adjusting the defaults, bias
correction, skull stripping the brain, segmenting and then normalizing.
I'll be happy to send the steps to you if you want, but the bottom line was
it didn't work all the time.
The best solutions we have found are:
1) Normalize the Functional image and apply that to the T1. Yes the
functional images have a geometric distortion relative to the T1 but it
isn't as bad as the artifact you get from normalizing the T1. Yes the
functional images have a much coarser voxel size so this is not the thing
to do for VBM, but it works if the primary purpose is to normalize the
functionals and produce moderately accurate functional overlays. Also if
you acquire fieldmaps you can minimize the functional volume distortions.
2) I should mention that we had originally acquired the MPRAGE slices
axially. It seems that acquiring it sagittally works better or at least
moves the inhomogeneity away from the top of the head. So this is what we
are doing now for all T1's.
We have also tried acquiring both T1 and T2 images for multispectral
segmentation and this sometimes improves the gray matter segmentation and
then the normalization.
Anyway if you have further thoughts on this, or anyone else does, or
someone has an easily implemented T1 sequence that fixes this problem on
the Trio, I'd love to hear about it.
Best regards,
Darren
At 05:55 PM 8/19/2005, Kareken, David A. wrote:
>Hi all,
>
> I've been having a terrible time with spatially normalizing some T1
> (MPRAGE from a Siemens Trio) images, and every single subject has the
> same problem. I've research this on the mail base, and nothing seems to
> help much.
>
> First, the whole brain images are stretched high at the top (vertex),
> the occipital lobe/cerebellum are dragged down, and the y-axis is
> abnormally compressed. The first and third problems resolved when I
> segmented the brains, and registered gray matter to the gray apriori
> image, but the occipital lobe/cerebellum is still dragged down/distorted
> quite severely. That aspect seems untouched.
>
> I seem to have the 10/04 code fix to spm_normalise.m that addresses the
> Matlab 6.5 bug. Default masking doesn't seem to do anything. Quite
> frustrating!
>
> If you'd cc reply's to me, in addition to the mail base, I'd appreciate
> it. Thanks to any/all who can help.
>
>David K
>
>David A. Kareken, Ph.D., ABPP/ABCN
>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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