[Mrtrix-discussion] Encoding.b value questions

[Donald Tournier]

Hi JS,


I'm having some issues with my data, especially the encoding.b file
> generated after I performed the "mrinfo -grad" command-line.  Here is the
> situation.  First of all I'm working with the NIFTI format, so I have
> converted my data using the the "mrconvert" command.
> My paramaters used here is b=1000, direction=20, average=4.  When I look at
> the encoding.b file resulting from the "mrinfo -grad", we noticed that the
> values are repeting themselves every 20 lines in the first three columns
> for
> 4 times instead of being all different.  Is that supposed to be that way ?
>

Given that you have 4 repeats, this is exactly what I would expect. I
assume there is no averaging done on the scanner, and you end up with 80
volumes? If so, this is correct, you have 4 sets of the same 20 directions.
I'm not sure why you think this is odd, why would you expect to get
different values in the different repeats of your gradient directions?

What is more problematic is that with 20 directions, you're not going to
get good results with CSD - particularly with a b-value of only 1000. Why
are you acquiring 4 repeats of 20, and not a full set of 80 unique
directions? Is there any scope for changing the acquisition parameters? If
so, I would strongly encourage you to increase the b-value to at least
2000s/mm², and acquire a minimum of 60 unique directions to get adequate
sampling over the orientation domain.


>
> I executed the "estimate_response" function but the values are way out of
> this world: 5.62455e+77 -9.96597e+75 3.52424e+76 -4.63953e+76 -3.93348e+75
> 7.96634e+76.  A colleague of mine noticed that the lmax was equal to 10
> when
> I performed the "disp_profile" rendering suggesting that maybe mrtrix was
> considering that my data had 80 directions instead of 20.  Is that good
> reasoning ?
> How can I go around this problem ?
>

Yes, MRtrix only looks at the number of 'directions' in the directions
file, and uses the lmax value assuming all these directions are unique.
This will obviously not work where there are repeats in the DW scheme. In
your case, you should specify "-lmax 4" to estimate_response, since this is
the maximum you can characterise with 20 directions: lmax=4 requires 15
directions, lmax = 6 requires at least 28 directions.

Hope this helps,

Cheers,

Donald.



> Thank you very much for your help,
>
> JS
>
>
>
>
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>


-- 
*Dr Jacques-Donald Tournier
*
Research Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg  Vic  3084
Ph:  +61 3 9035 7033
Fax:  +61 3 9035 7307
www.florey.edu.au
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