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> 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 langua!
ge 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 tr!
actography 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 w!
ant 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 probabil!
istic tractography
> with multiple masks, identified the two mas
ks, 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 asymme!
try 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 asym
metry 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 tha!
t 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&!
amp;id=N20nnxByjVAC&oi=fnd&pg=PT9
> &dq=Diffusion+MR
I+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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