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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