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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 > ------------------------------------------------------------------------- > > > >