[Mrtrix-discussion] COD on DTI data with 30 directions

[Thijs Dhollander]

Hi Marica,

This mailing list is dying a slow death...  We've got a brand new website,
www.mrtrix.org , which comes with an equally brand new community forum:
http://community.mrtrix.org
It'd be best to ask your question again over there: it's a better way of
archiving questions/answers over time, so users can benefit and contribute
more easily.

As a quick placeholder for an answer to your question: it is definitely
expected that the response at b=1000 is much more "fat" (less disk-y) than
the one at, e.g., b=3000.  However, we've recently come across several less
than optimal results from the dwi2response program ourselves, and in my
personal opinion, these specific issues are only bound to get (much) worse
at low b-values (we consider b=1000 to be a "low b-value").  That CSD still
performs well, is rather related to the fact that CSD is quite resilient to
small calibration errors of the response function... or at least if all you
expect is a "relatively ok-ish" outcome.  If you want the best outcome, it
suddenly becomes much more important to nail that calibration.  And even if
your FODs are not *that* great, whole brain tracking might still look
pretty fine after all, since tracking introduces extra constraints (e.g.,
curvature and minimum track length), that make it even harder to generate a
majority of really wrong tracks.

So all in all: the tractogram has a tendency to (too) easily look
"ok-ish".  I'd say: head on over to the community forum at
http://community.mrtrix.org , and add a screenshot of your actual FODs
(using the ODF display tool in mrview), and I'm sure you'll get some
interesting feedback (and maybe spark a discussion or two ;-)).

Cheers,
Thijs

On 23 February 2016 at 01:48, macara.p at libero.it <macara.p at libero.it> wrote:

> Hi,
>
> I would like to apply the constrained spherical deconvolution on my DTI
> dataset (30 directions, b=1000, 1 b0 image).
> I tried to compute the response function with the command dwi2response an
> it gave me the response function I attached in this screenshot
> ("response.png").
> Do you think it is correct? I have further run the CDS (dwi2fod) that gave
> me the image in my second screenshot ("CSD.png").
> I have also run the tractography (SD_stream) and it seems to me that it
> worked well ("tracto.png"), but I was wondering if doing the CSD makes
> sense given the type of data and the response function I get.
>
> Thanks,
> Marica
>
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>
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