JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for FSL Archives


FSL Archives

FSL Archives


FSL@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

FSL Home

FSL Home

FSL  January 2014

FSL January 2014

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Values in matrix1 after probtrackx

From:

Matt Glasser <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Sun, 19 Jan 2014 11:35:26 -0600

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (312 lines)

This can be seen from the technical papers that describe the fiber
orientation and tractography method, particularly Behrens et al 2003 and
Behrens et al 2007.

On 1/19/14 6:31 AM, "Meoded, Avner (NIH/NINDS) [E]" <[log in to unmask]>
wrote:

>P.s
>
>You mentioned that FA does not have direct influence on tractography, can
>you give a reference for that?
>
>Thank you
>
>Avner
>
>
>On 1/18/14 6:51 PM, "Matt Glasser" <[log in to unmask]> wrote:
>
>Hi Paul,
>
>That was a potential explanation for what might seem like
>counter-intuitive results I just thought up on a Saturday morning (there
>might be plenty of others!).  I suppose someone could test if this effect
>is real by looking at the HCP data and comparing a group with the
>smallest brains to a group of the largest brains.  One important variable
>would be whether the data were seeded from standard space (in which case
>the number of streamlines sent out would be constant across subjects) or
>native space (where the number of streamlines sent out would vary and
>potentially counteract the effect because a bigger brain would have more
>seeded streamlines).
>
>Peace,
>
>Matt.
>
>From: Chou Paul <[log in to unmask]>
>Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>Date: Saturday, January 18, 2014 5:36 PM
>To: <[log in to unmask]>
>Subject: Re: [FSL] Values in matrix1 after probtrackx
>
>Dear Matt
>
>According to your last point of the reply, are there any references or
>approaches about how to adjust for the "smaller brain" issue in such
>tractography research ? I am focus on neurodegenerative disease and this
>problem seems very important to this field. Would you provide me some
>advices on this issue ?
>
>Thank you
>
>Best
>
>Paul
>
>> Date: Sat, 18 Jan 2014 12:39:51 -0600
>> From: [log in to unmask]
>> Subject: Re: [FSL] Values in matrix1 after probtrackx
>> To: [log in to unmask]
>>
>> I've certainly found both Mark and Tim to be extremely helpful over the
>> years and have learned an enormous amount from both of them.  I know it
>>is
>> greatly appreciated when support requests are directed to the public
>> e-mail list (so that others may benefit from and participate in the
>> discussion).
>>
>> The relationship between the number of streamlines sent out from an ROI
>> that reach another and the number (let alone mention functional
>>influence)
>> of axons is not yet well characterized.  It's worth keeping in mind that
>> FA (and more advanced measures like f1, f2, and f3) do not have any
>>direct
>> influence on tractography.  Tractography is based on sending out some
>> number streamlines and following samples of fiber orientation
>> distributions until some stopping criterion is reached (like a stop
>>mask,
>> exceeding a curvature threshold, looping back on a region previously
>> traveled, etc). Streamlines do not increase in number depending on the
>> number of steps (i.e. distance) the tractography algorithm needs to take
>> between seed and target.  One starts with a fixed number (that you set
>> when running probtrackx) and this represents the maximum possible value
>> you could get (if all streamlines travelled the whole distance between
>> seed and target ROIs).
>>
>> The two main applications where it has been successfully used are to
>>build
>> spatial uncertainty distributions of pathways (where the voxels with the
>> largest number of streamlines represent the higher probability of a
>> pathway being located there and the voxels with fewer numbers of
>> streamlines represent lower probability of a pathway being located
>>there.
>> The other is making comparisons between streamline counts in the same
>> individual, where many uninteresting factors that influence streamline
>> counts are controlled for.
>>
>> The use of tractography to produce grey matter to grey matter structural
>> connectomes is a relatively recent one.  Interpreting these results
>>across
>> individuals or between patients and controls relative to the various
>> potential confounds is quite challenging.  In this case, the explanation
>> could be as simple as the subjects with neurodegenerative disease have
>> smaller (atrophied) brains and therefore the distance between ROIs is
>> reduced, which would increase streamline counts because streamline
>>counts
>> decrease with increasing distance in a log-linear fashion (more steps
>> means more chances to be stopped/diverted away from the target).
>>
>> Peace,
>>
>> Matt.
>>
>> On 1/18/14 7:30 AM, "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

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager