Hi Kristen
going over the posts for the last weeks after being on leave and this
one caught my eye...
my last paper just got rejected and one of the key criticisms was that i
hadn't provided enough detail regarding the tractography methodology.
specifically the reviewer commented that he/she did not understand what
"waytotal" means and could not understand why I used the exact tract
thresholding I did and went on to call my methods "dubious". my advice
is to overdescribe. unfortunately the FSL email list is currently not a
valid reference...
s
Lindgren, Kristen, Ann wrote:
> Thanks, Matt. I've already done all of my analyses using the waytotal
> for normalization as you and previous posts mentioned. My main
> concern was citing this method since I'm ready to submit my paper.
> Since Andreas asked about the asymmetry component, though, I was just
> letting him know what I did in case he had any thoughts. Like I said,
> you guys and others on this list were instrumental in me figuring out
> how to analyze my data, and I've included a shoutout to you in my
> acknowledgements. Thanks!
>
> Kristen
>
>
>
> -- Sent from my Palm Pre
>
> ------------------------------------------------------------------------
> Matt Glasser wrote:
>
> If you just want information on how to do it, Andreas and I have had
> extensive discussions on this list before, so you could search for
> “waytotal” and either of our names for that info.
>
>
>
> Peace,
>
>
>
> Matt.
>
>
>
> _____
>
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of LiuYan
> Sent: Monday, January 18, 2010 7:26 AM
> To: [log in to unmask]
> Subject: Re: [FSL] AW: [FSL] Publications normalizing tractography
> using waytotal
>
>
>
> Hi,
>
> Thanks Matt and Andreas for your response!
>
> Actually, I have the same question as Kristen, we have done a study by
> using probabilistic tractography, and now we need to put some
> references on our methods-- what is the normalization by waytotal.
> However, some pages are omitted from Brehens' Book by google preview,
> and we didn’t find any published references which have used and
> explained the waytotal normalization. We have to reply the reviews
> questions in a limited period; could you give us some other information?
>
> Regards,
>
> Yan
>
>
> > Date: Sat, 16 Jan 2010 18:15:10 +0100
> > From: [log in to unmask]
> > Subject: [FSL] AW: [FSL] Publications normalizing tractography using
> waytotal
> > To: [log in to unmask]
> >
> > 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
>
> _____
>
> 使用新一代 Windows Live Messenger 轻松交流和共享！
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>
--
========================
Scott Kolbe
MSRA Postdoctoral Fellow
Neuroimaging Group
Florey Neuroscience Institutes
Parkville, VIC, Australia, 3010.
ph: +61 3 8344 1879
email: [log in to unmask]
website: www.neuroimaging.org.au/index.php?id=383
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