Hi Mathias,
You may also want to check that the orientation of your input is FSL-friendly. I used to have a problem with this with the orientation being different from the FMRIB52 brain, which force-registered my cerebellums into the frontal lobe!
Since you're dealing with infant brains, you could also create your own cohort-specific template and use that with -t to troubleshoot...
Cherif.
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Cherif P. Sahyoun HST-MEMP
Developmental Neuroimaging of Cognitive Functions
C: 617 688 8048
H: 617 424 6956
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"Live as if this were your last day. Learn as if you'll live forever"
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On Mon, Oct 20, 2008 at 9:15 AM, Gwenaëlle DOUAUD
<[log in to unmask]> wrote:
Hi Mathias,
which version of FSL are you using? Your images seem to be fine for TBSS, so there should not be any problem. What happens if you use the -T option instead of the -n one?
Cheers,
Gwenaelle
--- En date de : Lun 20.10.08, Mathias Engstrom <[log in to unmask]> a écrit :
> De: Mathias Engstrom <[log in to unmask]>
> Objet: [FSL] TBSS Image quality
> À: [log in to unmask]
> Date: Lundi 20 Octobre 2008, 14h22
> Hi everybody,
>
> When running TBSS, are there any general requirements in
> terms of image
> quality that should be considered? We have a long running
> study on infants
> where there is a 15-dir (b=700 Voxel=1.4x1.4x2.2mm, TE/TR =
> 74/9000) diffusion
> scan included, on which we would like to use TBSS.
>
> A problem we keep on running into is that "tbss_2_reg
> -n" rotates our volumes
> and parts of the brain are being cropped. Tracts seem to
> have lined up, but
> the rotations are very unsatisfactory and alarming. In
> order to avoid these
> problem we have tried pre-normalization and exclusion of
> individuals with
> e.g. large ventricels, but the it does not seem to change
> anything.
>
> Is there anyone else who has been experiencing these
> problems? or know what
> they can originate from?
>
> If someone would like to take a further look I can gladly
> send you some
> exmaples (Attached png got reject due to size...).
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