[Mrtrix-discussion] csd equivalent of FA

[Alessandro Calamuneri]

Hi Donald,
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...
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?

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
>>>>
>>>>
>>>> _______________________________________________
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>>>> Mrtrix-discussion at www.nitrc.org
>>>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>>>
>>>>
>>>
>>
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