Hi Eric,
Since warping only the segmented gray matter still produced the same errors, would it be safe to assume that the skull stripped would do the same?
> -----Original Message-----
> From: Eric Zarahn [mailto:[log in to unmask]]
> Sent: Monday, August 22, 2005 2:04 PM
> To: Kareken, David A.; [log in to unmask]
> Subject: Re: [SPM] Spatial Normalization Problems w/ SPM2
>
>
> Dear David,
>
> I have found that skull/scalp stripping along with providing
> a little help to the starting estimates tends to eliminate
> unreasonable warping due to spatial normalization in most
> cases (normalizing to a skull/scalp stripped template).
>
> Best,
> Eric
>
>
>
> ----- Original Message -----
> From: "Kareken, David A." <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Saturday, August 20, 2005 10:34 AM
> Subject: Re: [SPM] Spatial Normalization Problems w/ SPM2
>
>
> > >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.
> >
> > Thanks, Darren. I might indeed be interested in the long route
> > solution
> you came up with.
> >
> > I did try doing just the EPIs, and was impressed how well
> it worked.
> > My
> main concern here is the stretching of orbital signal. It
> seems to want take preserved signal in the orbital area and
> stretch it downward to fill the signal void. Maybe just
> apply fewer non-linear itterations?
> >
> > By the way, our design required getting 4 MPRAGE scans on different
> > days--
> even after registering/averaging the four image volumes
> (which markedly improved the inhommegeniety of which you
> spoke to barely detectable visual levels), it still committed
> the same sins.
> >
> > -----Original Message-----
> > From: Darren Gitelman [mailto:[log in to unmask]]
> > Sent: Fri 8/19/2005 7:11 PM
> > To: Kareken, David A.
> > Cc: [log in to unmask]
> > Subject: Re: [SPM] Spatial Normalization Problems w/ SPM2
> >
> >
> >
> > 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
> > >
> > >
> >
> >
> >
> ----------------------------------------------------------------------
> > ---
> > 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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