[Mrtrix-discussion] Human Connectome data

[J-Donald Tournier]

Hi Anna,

Just to add to what Rob said, it might help if you gave us a breakdown of
exactly what commands you issued from getting the original HCP data all the
way to the csdeconv command. As Rob said, it looks like something funny has
happened to your DW gradient table, and it's hard to speculate as to what
that might be. Best just to tell exactly what you did rather than us try to
guess from the end result...

Cheers,
Donald

--
Dr J-Donald Tournier (PhD)

Senior Lecturer, Biomedical Engineering
Division of Imaging Sciences & Biomedical Engineering
King's College London

A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
T: +44 (0)20 7188 7118 ext 53613
W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering

On 29 Sep 2014 08:04, "Robert Smith" <robert.smith at florey.edu.au> wrote:

> 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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