[Mrtrix-discussion] Crossing-fibers gray matter CSD

[Wim Otte]

Hi Donald,

Converting the reference.nii does the job! Thanks.

Before running CSD on all gray-matter ROIS, I did some testing of the
streamtrack application.

What I notice is some straight line of high probability voxels through
the brain (from one hemisphere to the other; without running through
an anatomical struture). I know that false positives are still a
problem to be solved in fiber tracking (review D. Jones), but I just
want to ask if other people (using human data for example) encounter
the same thing.

I attached some screenshots from mrview (fODFs with ROI) and fslview
(fa with tracks2prob result 1% - 100%).

Is it normal to get these cross-like connectivities using prob. fiber tracking?

Wim Otte



On Wed, Apr 8, 2009 at 3:11 AM, Donald Tournier <d.tournier at brain.org.au> wrote:
> Hi Wim,
>
> Yes, in theory, tracks2prob should just copy the layout from the
> reference image. But it so happens that the NIfTI image handling
> routine overrides the layout and sets it to +0,+1,+2. There is no
> point in trying to use mrconvert to change the layout for a NIfTI
> image, it will always end up with the same result. What you could do
> is mrconvert the reference.nii image, and then the layouts will both
> be +0,+1,+2. Does that sound like a workable solution?
>
> I might try to make the NIfTI handler honour the layout specification,
> but that won't be ready for some time...
>
> Regards,
>
> Donald.
>
>
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