[Mrtrix-discussion] Crossing-fibers gray matter CSD

[Donald Tournier]

HI Wim,

These are some of the strangest tracking results I have seen so far!
On the other hand, it looks like you are tracking through cortex, so
maybe that could explain a few things. The main orientations look OK,
even in the cortex (I assume this is a very young animal). I'm
surprised that the non-radial directions in the cortex are so
consistent - they all seem to be pointing at 45°. Not too surprised
that the tracking down to the white matter stops so abruptly: the
tracks would need to bend quite sharply to get into the corpus
callosum. You might want to relax the curvature constraint if that's
want you're trying to get.

I don't have that many answers to this. Maybe there was a mistake in
the tracking? The FODs look OK on that coronal, but they do look odd
on the axial (not sure if I'm getting the slice orientations correct,
I'm used to human brains...). Are you using the correct file for the
tracking? Maybe you can copy/paste your entire command-line session to
see I can spot a problem somewhere...?

Another problem could be some non-uniformity in the gradient
directions you use in your acquisition. That might cause strangely
consistent directions to appear that would otherwise be random noise.
Could you post your gradient encoding file? It's a text file with 4
columns in it, it might be called 'encoding.b'. If you don't have it,
that information might be stored in your dwi.mif file, you can extract
it with this command: "mrinfo dwi.mif -grad encoding.b".

Cheers,

Donald.


On Thu, Apr 9, 2009 at 7:25 PM, Wim Otte <wim at invivonmr.uu.nl> wrote:
> 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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>



-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078