[Mrtrix-discussion] csd equivalent of FA

Thu May 28 12:42:04 PDT 2015

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*
*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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