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

Sun Apr 3 16:24:10 PDT 2016

Hi David,

So I guess this is where the issue of quantification becomes a matter of
debate. As was shown quite comprehensively by Derek Jones et al
<http://www.ncbi.nlm.nih.gov/pubmed/22846632>, streamlines counts are not
in themselves particularly meaningful - and hence can't be viewed as
quantitative. There is also evidence that they're not particularly
reproducible (at least when using probabilistic streamlines without an
enormous number of streamlines) - see e.g. our TDI paper on the issue
<http://www.ncbi.nlm.nih.gov/pubmed/24246491>. This is what I meant when I
said there isn't much quantification you can do in MRtrix 0.2. You have a
lot more options in MRtrix3, including ACT
<http://www.ncbi.nlm.nih.gov/pubmed/22705374>, SIFT
<http://www.ncbi.nlm.nih.gov/pubmed/23238430>, SIFT2
<http://www.ncbi.nlm.nih.gov/pubmed/26163802>, and AFD
<http://www.ncbi.nlm.nih.gov/pubmed/22036682> - SIFT being
particularly beneficial
for connectomic analyses <http://www.ncbi.nlm.nih.gov/pubmed/25312774>.

As to your question: I don't think these minor inaccuracies in the
responses are going to make much difference at all to the tractography
itself. These are minor noise ripples in the low signal region of the
response - what makes a big difference is the overall size of the response
(this influences the scaling of the FOD), and how broad it is. But even if
it does have a minor effect on the FOD, this is unlikely to affect the
tractography a great deal, and is even less likely to influence any
comparisons you might make between subjects - I don't see how this could
introduce a bias between your groups, at worst you might lose a negligible
amount of statistical power. This of course all assumes that the procedure
you're using is the same for all subjects.

So I would run at lmax=8 without worrying too much about it... If you were
to switch to use some of the methods in MRtrix3, then this would indeed be
a different matter.

Cheers,
Donald.

On 1 April 2016 at 18:02, David Grayson <dgrayson at ucdavis.edu> wrote:

> Hey Donald,
>
> I am in fact doing quantitative analyses of number of pobabilistic
> streamlines connecting a given pair of regions, across subjects. So I would
> prefer to minimize variation in the rf across subjects.
>
> From your experience, would you expect one of these rf's to be more
> consistent across subjects?
> ------------------------------
> *From:* J-Donald Tournier <jdtournier at gmail.com>
> *Sent:* Friday, April 1, 2016 12:15:30 AM
> *To:* David Grayson
> *Cc:* mrtrix-discussion at www.nitrc.org
>
> *Subject:* Re: [Mrtrix-discussion] Response functions at lmax=6 vs lmax=8
>
>
> 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>*
>>>
>>> _______________________________________________
>>> Mrtrix-discussion mailing list
>>> Mrtrix-discussion at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>
>>>
>>
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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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