[Neuroimaging] Tractography normalization

Konstantinos Arfanakis arfanakis at iit.edu
Wed Aug 5 08:23:15 CEST 2015


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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