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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