[Mrtrix-discussion] csd equivalent of FA

[Dorian P.]

Hi folks,

May I pop in a couple of related questions. First, has anyone obtained
correlation between AFD and FA? I extracted once AFD/HMOA with another
software (not MRtrix) and the correlation with FA was very high 0.9+. I was
susprised by this at the time but didn't have time to follow up.

Second, pardon if I am not updated with recent development, but is
multi-tissue CSD similar to NODDI? What is the difference of the two?

Thank you.
Dorian

On Thu, May 28, 2015 at 3:42 PM, J-Donald Tournier <jdtournier at gmail.com>
wrote:

> Hello again,
>
>
>> I will read AFD related documentation in mrtrix3; you are right, I should
>> move to new release, but we have data already processed with old version
>> and doing csd fittings again would take quite long time...
>>
>
> Well, the version of CSD in MRtrix3 is much faster - I process a typical
> dataset in ~15s. And with the changes we have coming up, it'll go down
> further to ~6s... :)
>
> After a quick look at afd paper, I have only another question for you
>> related to rational of AFD. If you have one fiber population in a voxel its
>> intepretation is straightforward. But, provided you have two fiber bundles
>> "estimated" within a voxel, what could be a proper afd measure? Could
>> average of two fod amplitudes be the answer?
>>
>
> From my point of view, the interpretation of AFD is straightforward
> whether you have one or more fibre populations - it relates explicitly to
> each individual fibre population. I guess the issue you're having is that
> it's no longer a simple scalar per voxel - but then that is a clearer
> reflection of the reality than a simple scalar could give you.
>
> However, one option that you have available to you is to use the *total *AFD
> - i.e. the sum of the AFDs for all fibre populations. It is clearly less
> informative than the AFD per fibre population (i.e. the *fixel-wise*
> AFD), but if you must have a scalar per voxel, it would definitely be
> better than the average AFD (if you have 2 fibre populations in a voxel,
> their average AFD will be half that of the voxel next door that contains
> only one of the fibre populations, which is a very artificial difference).
> The total AFD is trivial to compute since it's the l=0 term of the CSD
> output - the first volume in the file (all other harmonics have zero
> integral over the sphere). This measure is actually a pretty good surrogate
> for neurite density - with the caveat that the CSD output is not very well
> normalised, so care would be needed to ensure data are comparable across
> subjects, as for the AFD itself. If performing non-linear registration to a
> common space, you will also have the issue of modulation to deal with,
> which is not trivial since ideally you should modulate according to the
> change in cross-sectional area across the fibre axis (as is done in AFD).
>
> So yes, there are options, but none are as simple as one might like...
>
> Cheers,
> Donald.
>
>
>
>>
>> Thanks again,
>> Alessandro
>>
>>
>>
>> 2015-05-28 18:54 GMT+02:00 J-Donald Tournier <jdtournier at gmail.com>:
>>
>>> Hi Alessandro,
>>>
>>> Well, at heart AFD really is only the amplitude of the FOD along the
>>> fibre direction of interest - actually, technically it's the integral of
>>> the FOD over the FOD peak. You can compute the FOD amplitude in the old
>>> version, but all the tools to compute the integral are in MRtrix3...
>>>
>>> Besides, to really do AFD justice requires some fairly complex
>>> preprocessing steps to ensure values can be compared across subjects, which
>>> we still haven't documented properly. They're all currently implemented in
>>> MRtrix3 - this is where all the development effort is going. While you
>>> probably could hack something together using the old version, my
>>> recommendation would be to upgrade and wait for the documentation to be
>>> updated (hopefully not too long after the ISMRM...).
>>>
>>> Even if you do want to stick with the old version, the steps required
>>> will at least be documented on the MRtrix3 wiki, so you'll be able to see
>>> for yourself how feasible this might be...
>>>
>>> Cheers,
>>> Donald
>>> On 28 May 2015 5:41 pm, "Alessandro Calamuneri" <alecalamuneri at gmail.com>
>>> wrote:
>>>
>>>> Hi Donald,
>>>> thanks for quick answering..
>>>> Given I am using old mrtrix version (0.2), what could be a pipeline for
>>>> calculating AFD?
>>>>
>>>> Thanks,
>>>> Alessandro
>>>>
>>>> 2015-05-28 18:03 GMT+02:00 J-Donald Tournier <jdtournier at gmail.com>:
>>>>
>>>>> Hi Alessandro,
>>>>>
>>>>> Yes, that particular question has come up many times over the years...
>>>>> I think we have a suitable answer now: apparent fibre density (
>>>>> http://www.ncbi.nlm.nih.gov/pubmed/22036682). And this will probably
>>>>> be improved further using multi-tissue CSD (
>>>>> http://www.ncbi.nlm.nih.gov/pubmed/25109526)...
>>>>>
>>>>> Hope this answers your question.
>>>>> Cheers,
>>>>> Donald
>>>>> On 28 May 2015 4:00 pm, "Alessandro Calamuneri" <
>>>>> alecalamuneri at gmail.com> wrote:
>>>>>
>>>>>> Hi mrtrix experts,
>>>>>>
>>>>>> I would like to know whether there exists a csd based measure that
>>>>>> might be considered the equivalent of Fractional Anisotrpy.
>>>>>>
>>>>>> Best Regards,
>>>>>> Alessandro
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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 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>*
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