[Mrtrix-discussion] Crossing-fibers gray matter CSD

Mon Apr 13 05:37:43 PDT 2009

Hi Donald,

Indeed strange tracking results... I attached several files:
- screenshot: the first and second principal eigenvectors, constructed
with FSL, overlaid on the FA-map ('ground truth'...).
- screenshot: response function estimated in white matter voxels
- encoding.txt: (constructed from bvals and bvecs using the script
combine_bvecs_bvals.pl)
- csd_steps.sh: script used to construct fibers from the gray-matter seed.

Great that you are willing to check these files!

Wim

On Mon, Apr 13, 2009 at 4:29 AM, Donald Tournier
<d.tournier at brain.org.au> wrote:
> 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.
>>>
>>>
>>
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>
>
>
>
> --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9496 4078
>
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