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

[Dorian P.]

I always used to correct manually the single fiber mask. The automatic
thresholding includes out of brain voxels in inferior slices. A simple
threshold is not to be trusted, I think.

Dorian

On Tue, Mar 22, 2016 at 6:01 PM, J-Donald Tournier <jdtournier at gmail.com>
wrote:

> 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
> <%2B44%20%280%2920%207188%207118%20ext%2053613>*
> *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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