[Mrtrix-discussion] Human Connectome data

[Robert Smith]

Hmmm... Looking at those pancake-shaped FODs in the ventricles, my best
guess is that you've tried to manually extract only the DWIs corresponding
to a particular b-value, but erroneously included one volume with a lower
b-value (and with a diffusion sensitisation direction normal to those
pancakes). I'd check your extracted DWI volumes to see if one is much
brighter than the others; also run dwi2SH on the extracted volumes and
check the result in the viewer orientation plot, make sure the diffusion
profile shapes are correct. This should hopefully fix the tractography
problem.

(P.S. MRtrix3 has a command for automatically extracting DWI volumes
corresponding to a particular b-value shell... just sayin' :-P )

In terms of the FOD asymmetry, it looks to me as though there's a strong
bias field left-right (check out the sizes of the erroneous FODs in the
ventricles). I'd have a peek at any HCP-provided pre-processing images that
may be there, or calculate and visualise the mean DWI intensity across
volumes for the shell you're analysing, maybe an explicit bias field
correction has been performed on the DWIs and has gone wrong. But it's
tough to speculate on those FOD geometry asymmetries until the weird
ventricle FODs have been solved.

Rob


--

*Robert Smith, Ph.D*
Research Officer, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au

On Sat, Sep 27, 2014 at 7:00 AM, Anna Varentsova <avarents at gmail.com> wrote:

>  Dear all,
>
>  I am trying to analyze Human Connectome data and faced some issues.
> Tractoraphy results show lines in X-Y plane (
> http://postimg.org/image/depga0wul/). I checked FOD field (
> http://postimg.org/image/za93ht1lb/). FODs on the left-hand side and
> right-hand side do not look the same. I am not sure what can be causing
> this effect.
>
>  I have seen previous discussion about Human Connectome (
> http://www.nitrc.org/pipermail/mrtrix-discussion/2013-January/000626.html),
> but didn't see this issue to be reported before.
>
>  Thank you,
>  Anna
>
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