[Neuroimaging] Tractography normalization

[Eleftherios Garyfallidis]

Hi JB,

I am not familiar with the restrictions of the license. I think that
Konstantinos is the best person to answer this question. I am cc'ing him.

You may want to continue this discussion in a different thread as it is a
bit off topic.

Cheers,
Eleftherios

On Tue, Aug 4, 2015 at 9:42 PM, JB Poline <jbpoline at gmail.com> wrote:

> Hi,
>
> I was curious about the IIT license: does anyone understand
>
> "
> (2) You may not alter, transform, adapt or build upon the information,
> images or data;
> "
>
> so : "build upon the information" is a bit vague : I guess you cannot
> create an atlas or anything from it, you have to use it as it is ? That
> seems bad - but may be I missed something ?
>
> cheers
>
> JB
>
>
>
> On Tue, Aug 4, 2015 at 6:25 PM, Eleftherios Garyfallidis <
> garyfallidis at gmail.com> wrote:
>
>> Hello,
>>
>> On Tue, Aug 4, 2015 at 7:21 PM, Jorge Rudas <jrudascas at gmail.com> wrote:
>>
>>> Thanks for your answer Eleftherios
>>>
>>> One questions more...
>>>
>>> Be happy to ask as many questions as you need until everything is clear.
>> I am sure you will need
>> feedback from us to perform such an analysis. That is because although we
>> are currently working on making
>> easy workflows, right  now you will need write your own scripts combining
>> different DIPY tutorials of the
>> development version.
>>
>> Of course I am more than happy to help you with this.
>>
>>
>>> When you say "then apply the deformation fields to the tractographies",
>>> what exactly does this mean ?
>>>
>>> You will generate streamlines and FA maps in the native space of every
>> subject. Then you can for example register
>> the FAs to an FA template. After you have performed this registrations
>> you will also have saved the deformation fields
>> which were applied to the FAs so that they can be registered to the FA
>> template. Because the tractographies were
>> in the same space (native) as the FAs the same deformation fields can be
>> used to warp them to the FA template space
>> and in that way your tractographies will also be normalized.
>>
>> Cheers,
>> Eleftherios
>>
>> p.s. As an FA template I recommend using the IIT atlas.
>>
>>
>>> Regards
>>>
>>>
>>> *Jorge Rudas*
>>>
>>>
>>> 2015-08-04 15:55 GMT-05:00 Eleftherios Garyfallidis <
>>> garyfallidis at gmail.com>:
>>>
>>>> Hi Jorge,
>>>>
>>>> This is a very active research area in DIPY. There are currently two
>>>> ways:
>>>>
>>>> a) You can register FA images together using our image registration
>>>> functions and then apply the deformation fields to the tractographies.
>>>>
>>>> b) Segment bundles from the tractographies (manually or automatically)
>>>> and register them directly using the SLR. Paper here
>>>>
>>>> http://www.ncbi.nlm.nih.gov/pubmed/25987367
>>>>
>>>> Cheers,
>>>> Eleftherios
>>>>
>>>>
>>>>
>>>> On Tue, Aug 4, 2015 at 4:14 PM, Jorge Rudas <jrudascas at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi everyone
>>>>>
>>>>> Any suggestions for to spatial normalization of tractographys?. I want
>>>>> compare tractographys at population level.
>>>>>
>>>>> regards,
>>>>>
>>>>> *Jorge Rudas*
>>>>>
>>>>> *National University of Colombia*
>>>>>
>>>>>
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>>>>>
>>>>
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