[Neuroimaging] Tractography normalization

Fri Sep 4 17:51:25 CEST 2015

Hi JB,

As you mentioned, one clause of the license for the IIT Human Brain Atlas says that "You may not alter, transform, adapt or build upon the information, images or data”. However, the purpose of this clause is solely for protection of the work (suggested by the IIT lawyers who prepared the license). It is not intended to pose restrictions to the community, as we hope that our colleagues will use this resource as a basis for further development. Therefore, we urge whoever is interested for example in “building upon” the IIT Human Brain Atlas to contact us and request a license that gives permission for their particular project. We have already done this with folks at Harvard as well as a company in California. The process was very fast. This can be done not only for faculty or companies, but also for students at any level, postdocs, and whoever else is interested. This is not a burden to us. We want to ensure that our publicly accessible resource is useful for further advancing neuroimaging technologies. 

Regards,
Konstantinos

-- 
Konstantinos Arfanakis, Ph.D.
Professor

Director, MRI Research
Department of Biomedical Engineering
Medical Imaging Research Center
Illinois Institute of Technology

Leader, Imaging and Bioengineering Studies
Rush Alzheimer's Disease Center
Rush University Medical Center

www.iit.edu/~mri
www.twitter.com/MRIatIIT

office: (312) 567-3864
fax: (312) 567-3225

> On Aug 12, 2015, at 6:59 PM, 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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>>>> 
>>>> 
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>>> 
>>> 
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>> 

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