Did I write that?
I think a better explanation is on page 434-436.
The normalization is different from thresholding and is performed on the fdt_path output. The waytotal is the total number of samples making it from seed to target.
Cheers-
Andreas
________________________________
Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von LiuYan [[log in to unmask]]
Gesendet: Freitag, 29. Januar 2010 17:18
An: [log in to unmask]
Betreff: Re: [FSL] Publications normalizing tractography using waytotal
Hi Andreas and Matt:
Thanks again for your useful advises! And now I have Tim's book on my desk!
If I well understood, could I explain the waytotal based normalization like this:
The original tracts were normalized by the waytotal-based threshold. The number of the tract samples that pass through the target mask was divided by the waytotal, which is the total number of sample streamlines and has not been rejected due to the exclusion masks. Then the obtained connectivity distributions were thresholded with a probability of **%.
Is that correct? Many thanks!
Have a good weekend!
Yan
> Date: Mon, 18 Jan 2010 15:09:32 -0600
> From: [log in to unmask]
> Subject: Re: [FSL] AW: [FSL] Publications normalizing tractography using waytotal
> To: [log in to unmask]
>
> I would strongly agree with Andreas's caution of using the FreeSurfer
> labels, especially when the arcuate is fairly easy to identify entirely and
> correctly in individual subjects (with 2 fiber probabilistic tractography,
> that is), whereas the exact definition of Broca's and Wernicke's areas are
> not even clear in the literature, let alone individual subjects. In my
> publications I have tended to make the assumption that the terminations of
> the arcuate approximate locations of language related frontal and temporal
> cortex (and showed for a small meta analysis of temporal activations in
> language fMRI studies that this assumption is not crazy), rather than
> drawing ROIs where I think language cortex is and tracking the arcuate from
> these. The arcuate in my opinion is a readily identifiable anatomical
> structure with diffusion imaging like the thalamus is with structural
> imaging, whereas the cortical areas involved in language cannot be directly
> identified anatomically (yet).
>
> I also agree that waytotal normalization might not be the way to go here,
> given that you are interested in the asymmetries of FA.
>
> To be able to comment more specifically and helpfully, it would be necessary
> to know what questions you are trying to answer with this analysis.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Andreas Bartsch
> Sent: Monday, January 18, 2010 2:38 PM
> To: [log in to unmask]
> Subject: [FSL] AW: [FSL] Publications normalizing tractography using
> waytotal
>
> Hi,
>
> >I defined these anatomically using labels from Freesurfer
> Oh, does Freesurfer distribute these? Or did you assume it's
> Wernicke's/Broca's by cytoarchitectonic labels?
> I guess I do not need to speel out the words of caution here (pertaining to
> Brodmann labelling, correspondence of BA labels to "real" functionals, the
> arcuate also connectingto Exner's etc etc).
>
> >Here's what I did and what I calculated...
> Sounds good - one possible way to do it.
>
> >We did not do this
> Well, that's the point. I guess I would have used Matt's method instead of
> the waytotal normalization. Simply because a) you have no prior knowledge to
> rely on that the arcuate really exists in the particular individual
> (imagine, for example, that a clear angular gyrus is not identified in every
> subject - maybe in just 66%, depending on the sample). and b) it sounds like
> you want to detect asymmetries (and not enforce symmetry because, for
> example, the tracking is adversely affected on one side due to some
> pathology) - so I would have used Matt's method in your case.
>
> Matt - any ideas?
>
> Cheers-
> Andreas
>
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von
> Lindgren, Kristen, Ann [[log in to unmask]]
> Gesendet: Montag, 18. Januar 2010 18:17
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] Publications normalizing tractography using
> waytotal
>
> If I see you at a conference, I'll definitely buy you a beer :)
>
> i) how did you define Broca's / Wernicke's?
> I defined these anatomically using labels from Freesurfer
>
> ii) what asymmetry quotients did you compare?
> Here's what I did and what I calculated. Used probabilistic tractography
> with multiple masks, identified the two masks, one corresponding to Broca's
> area and the other to Wernicke's area, and checked off that seed space was
> not diffusion. This was done in each hemisphere. I then normalized the
> resulting fdt_paths for each subject and applied a constant threshold. I
> then binarized each normalized and thresholded tract and multiplied it by
> the participant's FA map. I then calculated average FA for the tract in each
> hemisphere for each participant. I ensured that I was only looking at white
> matter voxels by confining my calculations to those voxels that overlapped
> with the participant's white matter label from Freesurfer.
>
> For calculations, I looked at FA two ways. First I ran a MANOVA with FA as
> the dependent variable, group as the between-subjects independent variable,
> and hemisphere (left, right) as the within-subject independent variable.
> For the second analysis, I calculated an asymmetry quotient for FA using the
> formula (Left - Right)/[(Left + Right)/2]. These I compared with t-tests.
> I did not do volumetric analyses or assess volumetric asymmetries.
>
> iii) How did you ensure apriori that the arcuate actually exists?
> We did not do this and I'm not really sure how you would, but we based our
> assumptions that we would gather parts of this pathway based on previous
> literature about this pathway and its connections.
>
> I appreciate any thoughts you have. Thanks!
>
> Kristen
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Andreas Bartsch
> Sent: Sat 1/16/2010 12:15 PM
> To: [log in to unmask]
> Subject: [FSL] AW: [FSL] Publications normalizing tractography using
> waytotal
>
> When / where is the party;)?
>
> No - seriously, i) how did you define Broca's / Wernicke's? Anatomically,
> functionally, by ESM?; ii) what asymmetry quotients did you compare? As
> explained previously, the waytotal normalization enforces symmetry whereas
> Matt's approach may be more sensitive to asymmetries. How did you ensure
> apriori that the arcuate actually exists?
> >pull out the FA value of each individual voxel
> Sure - e.g. mask the FA volume by the (thresholded or unthresholded)
> fdt_path and write out all values into an ascii file (fsl2ascii) and then do
> whatever you want with it...
> Cheers-
> Andreas
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von
> Lindgren, Kristen, Ann [[log in to unmask]]
> Gesendet: Samstag, 16. Januar 2010 17:15
> An: [log in to unmask]
> Betreff: Re: [FSL] AW: [FSL] Publications normalizing tractography using
> waytotal
>
> Matt and Andreas, thanks for the info. I used probabilistic tractography
> between gray matter masks in Broca's and Wernicke's areas (so presumably
> parts of the arcuate fasciculus) and used the resulting fdt_paths mask to
> ascertain an average FA value across all of the voxels. I then compared the
> average FA values between two groups on each side and also compared
> asymmetry quotients. From earlier conversations, it sounded like waytotal
> thresholding was the best way to do this, whereas controlling for ROI size
> was better if I was looking at the volume of the resulting fdt_paths.
>
> Also, just out of curiosity, is there anyway to pull out the FA value of
> each individual voxel in each participant's fdt_paths instead of having to
> calculate an average FA across all voxels?
>
> Thanks again for all of your help! I seriously couldn't have finished my
> thesis without you guys!
>
> Kristen
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Andreas Bartsch
> Sent: Sat 1/16/2010 3:54 AM
> To: [log in to unmask]
> Subject: [FSL] AW: [FSL] Publications normalizing tractography using
> waytotal
>
> Hi,
>
> yep - it's part of the book. The underlying Bayesian formulas were taken out
> in the editing process, however. We have not made it - due to time
> constraints - to seperately publish it in a journal but will hopefully do
> this year.
> Anyway - it's not such a big deal: as described previously in the list, the
> waytotal i) depends on the prior that you know the tract is there (in the
> particular individual examined) and ii) does not alter the spatial extent of
> fdt_path itself but simply scales the values. Later, by thresholding you set
> a cutoff that impacts the spatial extent of the tract.
> So you have to ascertain prior to the tractography (!) and by other, e.g.
> clinical means, that you can be sure that the tract is there and you have to
> decide if you consider scaling by the waytotal appropriate prior to
> thresholding.
> Is it the spatial extent of the tract you are after, or some symmetry
> analysis, or the probability values themselves?
> Cheers-
> Andreas
>
> ________________________________________
> Von: FSL - FMRIB's Software Library [[log in to unmask]] im Auftrag von Matt
> Glasser [[log in to unmask]]
> Gesendet: Freitag, 15. Januar 2010 23:12
> An: [log in to unmask]
> Betreff: Re: [FSL] Publications normalizing tractography using waytotal
>
> Hi Kristen,
>
> I have not published any papers with this method yet, but Andreas Bartsch
> may have. I know the method is described in Heidi and Tim's book, in
> Andreas's chapter (19). The book (or at least part of it) is on Google
> books:
> http://books.google.com/books?hl=en&lr=lang_en&id=N20nnxByjVAC&oi=fnd&pg=PT9
> &dq=Diffusion+MRI+from+quantitative+measurement+to+in+vivo+neuroanatomy&ots=
> FTIbmZwxe3&sig=f8ySrMDRvk3gKbSvvVcZWX6ftik#v=onepage&q=&f=false
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Kristen Lindgren
> Sent: Friday, January 15, 2010 4:00 PM
> To: [log in to unmask]
> Subject: [FSL] Publications normalizing tractography using waytotal
>
> Hello. This question may be best answered by Matt Glasser, but I'm
> wondering if anyone is aware of a publication using probabilistic
> tractography and normalizing the results using the waytotal values. I'd be
> especially interested in ones looking at the arcuate fasciculus. Way back
> when when I was working on my thesis, Matt said that he was using this in
> his studies, but I'm not sure if he or any others have published using this
> method. I'm working on submitting my DTI paper and would love to have
> something more than "personal communication" to site when describing my
> method. Any thoughts or help is appreciated. Thanks in advance!
>
> Kristen
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