[Neuroimaging] Tractography normalization

[Konstantinos Arfanakis]

Hi JB,

I know my answer to your question, but let me first bring your question to our general counsel who wrote the text for the license.

Regards,
Konstantinos

> On Aug 13, 2015, at 2:59 AM, JB Poline <jbpoline at gmail.com> wrote:
> 
> Hi Konstantinos,
> 
> Say I want to derive a new atlas from IIT. Can I redistribute my
> derived atlas freely ?
> 
> cheers
> JB
> 
> On Tue, Aug 4, 2015 at 11:23 PM, Konstantinos Arfanakis
> <arfanakis at iit.edu> wrote:
>> Hi JB,
>> 
>> It would help me answer your question if you could give me a very general
>> description of what you are planning to generate and how would that be used.
>> 
>> Regards,
>> Konstantinos
>> 
>> 
>> 
>> On Aug 5, 2015, at 4:54 AM, Eleftherios Garyfallidis
>> <garyfallidis at gmail.com> wrote:
>> 
>> 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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>>>>> 
>>>>> 
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