Like I said, I learned a big chunk of what I know from the Oxford guys
including Mark and Tim. We are all very fortunate they wrote, have freely
shared, and supported such useful software.
Peace,
Matt.
On 1/19/14 4:07 PM, "Meoded, Avner (NIH/NINDS) [E]" <[log in to unmask]>
wrote:
>Look at Matt Glasser responses: concise, direct and full of useful
>information.
>
>
>
>On 1/19/14 4:25 PM, "Watson, Christopher"
><[log in to unmask]> wrote:
>
>> "Again, a long, not relevant answer to my question."
>>
>> You might find you'll have more success in getting help if you stop
>>being so
>> rude. Particularly to one of the top contributors to the list.
>> Most people who contribute to this list do so, presumably, because they
>> believe that for the advancement of science it is important to help
>>others in
>> their own research. However, you are not *entitled* to receive help,
>>yet you
>> have already received several long, thoughtful replies. On a Sunday, no
>>less.
>>
>> If you truly did read the diffusion textbook and the original research
>>papers,
>> and still have questions about reduced FA coinciding with increased
>> connectivity (per probabilistic tractography), then you should re-read
>>the
>> sources, study the FSL wiki (and the functions' help sections), and
>>read the
>> literature. This is not a rare topic.
>>
>> Chris
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of
>>Meoded,
>> Avner (NIH/NINDS) [E] [[log in to unmask]]
>> Sent: Sunday, January 19, 2014 7:34 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Values in matrix1 after probtrackx
>>
>> Dear Mark
>> Again, a long, not relevant answer to my question.
>> What about possible explanations related to probabilistic tractography
>>and
>> not related to corrected DTI data? From people who deal with
>>probabilistic
>> tractography every day
>>
>>
>>
>> Thank you
>>
>> Avner
>>
>>
>> On 1/19/14 3:09 AM, "Mark Jenkinson" <[log in to unmask]>
>>wrote:
>>
>>> Dear Avner,
>>>
>>> I am sorry that you were dissatisfied with my attempts to help you. I
>>> genuinely try to help everyone that I can on the list.
>>>
>>> When working from only a few lines in an email it is hard to not make
>>>some
>>> assumptions, but actually I do not like making assumptions and I try
>>>to avoid
>>> them. I did assume that you work for the NIH (based on your email
>>>address
>>> and
>>> sign-up name) and therefore were in contact with others in the NIH with
>>> experience in diffusion imaging and analysis. It is a pity if you do
>>>not
>>> have
>>> access to such people.
>>>
>>> I was not intending to imply that we could not provide you any
>>>information,
>>> but the situation that you described, with unintuitive results in an
>>> experiment with patients vs controls, requires very careful analysis
>>>and
>>> scrutiny to avoid making incorrect interpretations. This scrutiny
>>>would be
>>> beyond what we could provide in a few paragraphs of an email. Matt has
>>> explained something about what tractography gives you and provided one
>>> potential explanation, but as he points out himself there are other
>>> possibilities and the interpretation is quite challenging. In your
>>>case I
>>> think it is important to carefully investigate all potential factors
>>>that
>>> could drive the results, such as image quality (e.g. SNR), artifacts
>>> (including what remains after standard artifact correction), the
>>> anatomy/geometry of the brain areas you are investigating, as well as
>>>the
>>> biology of the particular pathologies involved. Given the many complex
>>>issues
>>> that can arise here, related to diffusion imaging, brain anatomy and
>>>biology
>>> (not just tractography), I recommended that you seek out someone who
>>>could
>>> look carefully through your data and talk to you about issues related
>>>to the
>>> data, the analysis, the anatomy and the biology involved in this
>>>particular
>>> study.
>>>
>>> I still recommend that you seek someone out to discuss these issues,
>>>since we
>>> cannot adequately cover these things by email. This is why I was
>>>suggesting
>>> that you find someone in the NIH, but it would not have to be someone
>>>from
>>> there. I make this recommendation because I honestly think it is
>>>important
>>> in
>>> order to make sure that you get a correct interpretation of your
>>>study. If
>>> you have very specific questions then we are happy to answer them, but
>>>I
>>> strongly encourage you to find someone to discuss your study with in
>>>detail.
>>>
>>> As for the response from Tim Behrens, I hope that you can appreciate
>>>that
>>> answering emails, writing documentation and textbooks is something
>>>that takes
>>> away from research time and that each of us makes certain sacrifices
>>>in order
>>> to do these things. We all have to decide on the nature and amount to
>>>which
>>> we can undertake such tasks. If we do not limit this time then we
>>>would not
>>> be able to do research, write papers and grants, and therefore stay
>>>employed.
>>> I try to give advice on the list that I feel is of most benefit given
>>>the
>>> limited time I have to answer such queries on what is quite an active
>>>email
>>> list. I hope that you can respect this situation and can believe that
>>>my
>>> emails were really intended to help, even if you were not happy with
>>>them.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>>
>>> On 18 Jan 2014, at 13:30, "Meoded, Avner (NIH/NINDS) [E]"
>>> <[log in to unmask]> wrote:
>>>
>>>> Dear Mark,
>>>>
>>>> I see you like to make assumptions. So let us assume that I am an high
>>>> school student who does not understand a thing about DTI. Moreover I
>>>>do not
>>>> understand the basics of probabilistic tractography. So in order to
>>>> understand more I read Diffusion MRI book (edited by Berg and
>>>>Behrens) and
>>>> also papers that deal with different tractography methods. So now I
>>>> understand a little bit of tractography but still there are unclear
>>>>issues
>>>> that I would like to clarify with the experts in the field- that is
>>>>the
>>>> reason I contacted FSL community.
>>>> If you see the title of my mail it is "Values in matrix1 after
>>>>probtrackx";
>>>> The specific question I have is what those values mean? Probabilistic
>>>> tractography aim to quantify uncertainty on the PDD and build a
>>>>connectivity
>>>> distribution. Now if you go and check matrix obtained from network1
>>>>option
>>>> in probrackx2 you will see that the matrix contain values in the
>>>>range of
>>>> 1-1,000,000 and beyond. You mentioned in you last e-mail that:
>>>>"Uncertainty
>>>> in direction at any point in the brain will enhance the uncertainty
>>>>in the
>>>> tractography from that point onwards for any tracks that pass through
>>>>that
>>>> point." How can we learn about this uncertainty from the matrix
>>>>values?
>>>>
>>>> Indeed at the NIH there are many experts who are always available for
>>>> discussion about all aspects of health and science. However, is
>>>> FSL/Probtrakcx a NIH application???
>>>>
>>>> Finally I would like to show Timothy Behrens's response to my
>>>>question :
>>>>
>>>> "if you have posted it to the FSL list then you should get an answer
>>>>soon.
>>>> It is a very effective community forum. You will understand that
>>>>with more
>>>> than 5000 users, there is no way I can personally answer every
>>>>question and
>>>> hope to maintain a research career!"
>>>>
>>>> This is the answer from the researcher who is the first author on the
>>>> NeuroImage paper from 2007 about probabilistic tractography, and also
>>>>the
>>>> one who wrote the chapter MR diffusion tractography with Saad Jbadi
>>>>in the
>>>> book mentioned above.
>>>>
>>>>
>>>>
>>>>
>>>> Avner
>>>>
>>>>
>>>> On 1/18/14 4:58 AM, "Mark Jenkinson" <[log in to unmask]>
>>>>wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Artifact "correction" methods don't fully remove all artifacts, so
>>>>>you
>>>>> cannot
>>>>> rule out the possibility that artifacts are causing the things you
>>>>>are
>>>>> seeing
>>>>> just because you have run artifact correction. Such methods remove
>>>>>a lot
>>>>> of
>>>>> the effect of artifacts but not absolutely everything.
>>>>>
>>>>> I'm not sure what you mean by "steps" but the samples in probtrack
>>>>>refer to
>>>>> individual streamlines (that are selected from the probability
>>>>>distribution
>>>>> of
>>>>> possible streamlines). Uncertainty in direction at any point in the
>>>>>brain
>>>>> will enhance the uncertainty in the tractography from that point
>>>>>onwards
>>>>> for
>>>>> any tracks that pass through that point.
>>>>>
>>>>> You definite cannot make categorical statements such as "more samples
>>>>> mean[s]
>>>>> more disease".
>>>>> As I said, there are a *lot* of things that can influence
>>>>>tractography
>>>>> results
>>>>> and you really should discuss you particular case, with your
>>>>>particular
>>>>> subjects and you particular data acquisition, with someone who is
>>>>> experienced
>>>>> with tractography. There certainly should be such people in the NIH.
>>>>>
>>>>> All the best,
>>>>> Mark
>>>>>
>>>>>
>>>>> On 17 Jan 2014, at 13:10, "Meoded, Avner (NIH/NINDS) [E]"
>>>>> <[log in to unmask]> wrote:
>>>>>
>>>>>> Hi
>>>>>> The raw DTI data was corrected for artifacts.
>>>>>> As you mentioned less uncertainty may enhance measures of
>>>>>>connectivity.
>>>>>> But
>>>>>> in my case I documented reduced FA and not increased FA, the latter
>>>>>>is
>>>>>> seen
>>>>>> perhaps in regions with reduced crossing fibers.
>>>>>> Now my question is specific to probabilistic tractography: number of
>>>>>> samples
>>>>>> obtained from probtrackx between to regions mean number of "steps"
>>>>>>track
>>>>>> does; are those "steps" depends on the uncertainty? So at the end
>>>>>>more
>>>>>> samples mean more disease?
>>>>>>
>>>>>> Thank you
>>>>>>
>>>>>> Avner
>>>>>>
>>>>>> On 1/17/14 7:39 AM, "Mark Jenkinson" <[log in to unmask]>
>>>>>>wrote:
>>>>>>
>>>>>>> Hi,
>>>>>>>
>>>>>>> These are not simple questions and it will depend a lot on the
>>>>>>>nature of
>>>>>>> your
>>>>>>> data - SNR, artefacts, amount of movement, etc. There are also
>>>>>>>some
>>>>>>> potential
>>>>>>> biological possibilities, such as reduction in crossing tracts,
>>>>>>>which can
>>>>>>> enhance measures of connectivity (since there is less uncertainty
>>>>>>>in the
>>>>>>> crossing region) without meaning that the axonal tract is
>>>>>>>biologically
>>>>>>> "stronger". You should look very critically at your data and show
>>>>>>>it to
>>>>>>> people who are experienced with diffusion analysis.
>>>>>>>
>>>>>>> All the best,
>>>>>>> Mark
>>>>>>>
>>>>>>>
>>>>>>> On 16 Jan 2014, at 18:08, "Meoded, Avner (NIH/NINDS) [E]"
>>>>>>> <[log in to unmask]> wrote:
>>>>>>>
>>>>>>>> Dear FSL users
>>>>>>>>
>>>>>>>> I conducted a study with network1 option and then did structural
>>>>>>>> connectome
>>>>>>>> analysis, in patients affected with neurodegenerative disease.
>>>>>>>> I also performed TBSS and found reduced FA values in different
>>>>>>>>areas in
>>>>>>>> patients compared to controls.
>>>>>>>> The problem is that I have higher values stored in the
>>>>>>>>connectivity
>>>>>>>> matrices
>>>>>>>> in patients compared to controls, and hence after connectome
>>>>>>>>analyses I
>>>>>>>> obtained networks that are more connected in patients. Now I know
>>>>>>>>that
>>>>>>>> these
>>>>>>>> values cannot represent axons, but how you can explain reduced FA
>>>>>>>>in
>>>>>>>> patients
>>>>>>>> and more streamlines evaluated in probtrackx? Or what are the
>>>>>>>>numbers
>>>>>>>> stored
>>>>>>>> in the matrix mean? (after running seed to seed network 1)
>>>>>>>>
>>>>>>>> Is this because in patients (with white matter disease, lower FA)
>>>>>>>>there
>>>>>>>> is
>>>>>>>> more uncertainty in voxels between roi1 and roi2 and therefore we
>>>>>>>>get
>>>>>>>> more
>>>>>>>> samples so basically tracts tend to spread more and as a results
>>>>>>>>more
>>>>>>>> sample?
>>>>>>>> so at the end more samples which represents more uncertainty
>>>>>>>>(disease)
>>>>>>>> Should I normalize the matrices in some way
>>>>>>>>
>>>>>>>>
>>>>>>>> Thank you
>>>>>>>>
>>>>>>>> Avner
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