[Camino-users] tractography on a normalized tensor data

[Binod Thapa Chhetry]

Hi Philip,

I realize the complications with tracking in MNI space. As you recommended,
I will try and run the Bayesian algorithm in native space DWI data.
How would one transform the resulting lines to MNI though?

Binod



On Wed, Aug 14, 2013 at 3:29 PM, Philip A Cook <cookpa at mail.med.upenn.edu>wrote:

> dtlutgen uses a single orientation for the test function, meaning that it
> won't account for any variance in uncertainty caused by the placement of
> the diffusion gradients. So I think using the same scheme file will be no
> worse overall. You can run dtlutgen with different random seeds to get a
> different orientation for the test function. Doing this a few times and
> then averaging the results would smooth out the lookup table parameters,
> but might be overkill.
>
> There's other issues with tracking in MNI space, particularly if there's a
> nonlinear transformation, in which case the reorientation of the tensors
> (and hence their relative orientation to the original gradients) would be
> variable anyway, also changes to the geometry of the tracts would likely
> influence results. Any changes in the anisotropy of the tensors due to
> interpolation will introduce differences in the estimated uncertainty.
>
> I agree the best way would be to track in subject space using the Bayesian
> algorithm and transform the resulting lines.
>
> On Aug 14, 2013, at 2:32 PM, Alexander, Daniel wrote:
>
> > Hi,
> >
> > Using the original schemefile is not perfect, but not unreasonable.  It
> is hard to think of a better way to do it if you really have to track in
> the MNI space.  The other option of course is to track in the native space
> and transform the streamlines into MNI space instead, which avoids some of
> these complications.
> >
> > Danny
> >
> >
> > On 9 Aug 2013, at 23:23, Binod Thapa Chhetry <bt2318 at columbia.edu>
> wrote:
> >
> >> Hi all,
> >>
> >> I want to run tractography with my tensors in a standard MNI space. I
> have normalized the fitted single tensor data(from dtifit) using DTI-TK.
> Now, I could do nifti2camino and bring my normalized tensor data(from
> DTI-TK) in nii to camino format.
> >>
> >> I was hoping if somebody could tell me what would be the
> best/appropriate input model for probabilistic tractography. Since, I have
> normalized tensors, I was thinking of PICO but then I only have schemefile
> for the tensor in native space, not in MNI. Can I use the same
> schemefile?Or, should I use a different model altogether, and how?
> >>
> >> Hope this is not too confusing.
> >>
> >> Looking forward for a reply.
> >> Binod
> >>
> >>
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> >
> >
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