[Mrtrix-discussion] Response functions at lmax=6 vs lmax=8

[J-Donald Tournier]

Hi David,

I've never heard of this being referred to as a 'nubbin', but it's clear
enough... ;)

Looking at your responses though, the 'nubbin' isn't all that worrying.
What's more worrying is the fact that the lmax=6 response is sharper than
the lmax=8 response, which seems wrong. Your lmax=8 response is certainly
broader than I'd expect at b=3000.

So all this suggests that the response function estimation isn't working
all that well, which is typically a symptom of a poor single-fibre mask.
You used an FA threshold of 0.7 here, but bear in mind that this is by no
means a 'default' - this is more of a guideline, as stated in the
documentation
<http://jdtournier.github.io/mrtrix-0.2/tractography/preprocess.html#csd>.
Here's the relevant excerpt:

Note that this value is a guide only - feel free to use a different value
> if this does not produce satisfactory results. Ideally, you should now have
> a mask containing a few hundred voxels, all located within high FA white
> matter regions. *It is very important to check that the single-fibre mask
> is suitable, as otherwise the response function produced in the following
> step may be totally inappropriate, which would seriously affect the quality
> of the CSD output*. If needed, you can edit this mask image to remove
> unwanted voxels using the ROI analysis
> <http://jdtournier.github.io/mrtrix-0.2/general/mrview.html#roi> sidebar
> tool within MRview
> <http://jdtournier.github.io/mrtrix-0.2/general/mrview.html>.


I would have a good look at the single-fibre mask used in this step, and
check against the above. The chances are you might find a lot of noisy
high-FA edge voxels got included or something, despite the erosion step.
This all depends on how good the initial brain mask was (I often found it
difficult to exclude the nasal sinuses, for example). Unfortunately, this
step can be a bit fiddly.

Alternatively, you could upgrade to MRtrix3 <http://www.mrtrix.org> - we've
put in quite a bit of work on estimating the response function
<http://mrtrix.readthedocs.org/en/latest/concepts/response_function_estimation.html>
...

All the best,
Donald.


On 22 March 2016 at 19:47, David Grayson <dgrayson at ucdavis.edu> wrote:

> Hi MRtrixers,
>
>
>
> I have HARDI datasets on a large sample of young adults (7-16yrs) taken
> with 72-dir and b0=3000. I am wondering whether I should proceed with
> lmax=6 or 8. I am using MRtrix 0.2.12.
>
>
>
> I am concerned about using lmax=8 because in the response function there
> is often a ‘nubbin’ that appears right in the center of the Z-axis line
> that doesn’t appear at lmax=6. The below link shows an example of the RF’s
> generated for a single subject taken at lmax=6 (on the left) and lmax=8 (on
> the right). These are generated using default parameters (FA threshold of
> 0.7 for the single-fiber-orientation mask).
>
> http://imgur.com/a/ODrcf
>
>
>
> Hopefully it’s obvious what I’m talking about. Sometimes this nubbin is
> more pronounced than what I’m showing here. I’m not sure how concerned I
> should be about this, but based on my intuition about what the RF means,
> the Z-axis itself should represent the global minimum of the DW signal,
> which is obviously not the case with lmax=8. Should I avoid any appearance
> of this effect at all costs, or is there some rule of thumb for how big it
> can be before I should be concerned about it?
>
>
>
> Thanks,
>
>
>
> David
>
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>


-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing'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
<http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering>*
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