Hi: How can I unsubscriber this mail? Thanks! > 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 _________________________________________________________________ Windows Live: Keep your friends up to date with what you do online. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_1:092010