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

Fri Apr 1 00:15:30 PDT 2016

Hi David,

Yes, these look fine. That's often a little protuberance like this in the
response, it'll be due to some extent to the Rician bias driving the signal
away from zero in this region. It's a minor inaccuracy that shouldn't make
a great deal of difference to the output of CSD. In fact, some people
reckon it provides a better fit to the actual signal (since it contains
Rician bias anyway), and yields sharper FODs... Not entirely sold on that
one, but just to say that it really shouldn't impact on any downstream
inferences.

On that note, these subtle differences and inaccuracies in the response may
conceivably make a difference if you're doing something quantitative with
the tracks themselves across subjects. There's really very little you can
do on that front with MRtrix 0.2. If you'd been using MRtrix3, there would
be many more options available for quantification, at which point you'd
need to worry about this. But even then, the main concern is to make sure
the same response is used across subjects, rather than whether the response
is perfect...

Hope this helps,
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 1 Apr 2016 4:39 am, "David Grayson" <dgrayson at ucdavis.edu> wrote:

> Thanks for the responses here.
>
>
> I should have mentioned, I have been using the freesurfer WM mask
> (co-registered to the B0) to exclude noisy voxels. Looks like there was an
> issue with co-registration. Now that this is fixed, indeed the lmax=8
> response looks (very slightly) sharper than lmax=6.
>
>
> However, I'm wondering if you can have a look at the following comparisons
> of lmax=6 vs lmax=8, using an eroded WM mask and using the full WM mask.
> The lmax=8 still produces the protruberance on the z-axis, which is
> exaggerated using the eroded WM mask. Does this suggest that I should
> perhaps stick with lmax=6, and avoid eroding any further the WM mask? Would
> you consider these RF's acceptable now?
>
>
> http://imgur.com/42NCktt
>
> Thank you very much,
>
> David
>
>
> ------------------------------
> *From:* albnet at gmail.com <albnet at gmail.com> on behalf of Dorian P. <
> alb.net at gmail.com>
> *Sent:* Tuesday, March 22, 2016 3:10 PM
> *To:* J-Donald Tournier
> *Cc:* David Grayson; mrtrix-discussion at www.nitrc.org
> *Subject:* Re: [Mrtrix-discussion] Response functions at lmax=6 vs lmax=8
>
> 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
>>>
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>
>>>
>>
>>
>> --
>> *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
>> <%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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>>
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