>
> > Thanks Doug. I wasn't clear in my DOSS question, I meant to ask why
> > are categoricalXcontinuous interactions (e.g. such as the one probed
> > by the contrast "Does the thickness-age correlation differ between
> > group A and B?") still created in DOSS analyses, when by definition
> > DOSS imposes that (e.g.) thickness-age correlations have the same
> > slopes for all groups?
> Do not use DOSS with QDEC. There is a bug in it that causes the
> contrasts to be in error at times
>
I am aware of the contrasts bug, and have noticed some contrasts that were
wrong, but I was just wondering whether the said contrast ("Does the
thickness-age correlation differ between group A and B?") was is in fact
ever meant to be computed, as it seems it should not be there by virtue of
the definition of DOSS.On 8 March 2014 00:04, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > On 03/07/2014 06:45 PM, Tudor Popescu wrote: > > Thanks Doug. I wasn't clear in my DOSS question, I meant to ask why > > are categoricalXcontinuous interactions (e.g. such as the one probed > > by the contrast "Does the thickness-age correlation differ between > > group A and B?") still created in DOSS analyses, when by definition > > DOSS imposes that (e.g.) thickness-age correlations have the same > > slopes for all groups? > Do not use DOSS with QDEC. There is a bug in it that causes the > contrasts to be in error at times. > > > > Two more questions: > > > > - If selecting the Volume-based radio-button in QDEC's Design tab, the > > Measure drop-down list is replaced with "Not yet implemented", but > > pressing Analyze still proceeds as normal and delivers the expected > > contrasts. What does "Volume" exactly refer to, in those contrasts, > > and how is that different to the "normalised volume" measured in > > voxel-based morphometry (VBM)? > It was supposed to be an analysis like a VBM where you are looking a > volume-structured data instead of surface-structured. > > > > - (Bailey, Zatorre, and Penhune 2013) say that "The thickness maps > > produced are not restricted to the voxel resolution of the original > > data and thus are capable of detecting submillimeter differences > > between groups". Is it really the case that the power of a > > surface-based analysis is completely independent of the resolution of > > the T1 images? Isn't the accuracy of the mesh dependent on the > > volumetric (T1) resolution? > > Bruce may want to weigh in on this one, but it is not the case that any > resolution will do. I think what they are saying is that the surface > placement (and so thickness est) is better than the voxel size (subvox > rsolution). This can be achieved because of smoothness constraints. > > doug > > > > > Thanks! > > Tudor > > > > > > On 6 March 2014 16:53, Douglas N Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > > > On 03/06/2014 10:35 AM, Tudor Popescu wrote: > > > Sorry, couple more questions: > > > > > > 1) I know that QDEC's/mri_glmfit's equivalent in FSL ("randomise") > > > applies the GLM by doing permutations, and so already corrects for > > > multiple comparisons in the process. How similar is this to what > > > Monte-Carlo does (i.e. controlling FWE via repeated simulations) > > upon > > > the initially uncorrected QDEC results? > > By default QDEC users the monte carlo simulation. FSL randomise can > do > > either monte carlo or permutaion. mri_glmfit-sim can also do > > permutation. > > > > > > 2) In FSL, a comparison between groups A and B is tested by > defining > > > both a "A>B" as well as a "B>A" contrast - the reason being (as > > far as > > > I understand) that taking the logical complement of "A>B", i.e. > > > inverting the t-values in the statistical map, is *not* equal to > the > > > map produced by the cotnrast "B>A". How come, then, that QDEC > > phrases > > > the group contrast in a "two-tailed" way (i.e. "do groups A and B > > > differ")? Is the dichotomy not necessary in QDEC, or is it > > simply done > > > behind the scenes? > > What do you mean by "inverting the t-values"? It is the same as > > changing > > the sign of the t values. In FS we preserve the sign in our "sig" > maps > > (sign(t)*-log10(p)). > > > > > > 3) I've read papers where the thickness from *native*-space was > used > > > in the analyses, even though initially T1-weighted images were > > > initially aligned to the ICBM 152 template. Why isn't thickness > from > > > this *standard*-space used, as happens in FSLVBM with grey matter > > > density? Why even register to the template in the first place if > > > you're then going to go back and use native-space values? > > I'm not sure what you mean here. If someone warped their T1 data > > to some > > template space and then computed thickness, then that thickness > > will not > > represent the thickness from the individual and the group stats > > will be > > skewed by this > > doug > > > > > > Thanks! > > > > > > > > > On 6 March 2014 10:20, Tudor Popescu <tud...@gmail.com > > <mailto:tud...@gmail.com> > > > <mailto:tud...@gmail.com <mailto:tud...@gmail.com>>> wrote: > > > > > > Thank you very much Doug. > > > Tudor > > > > > > > > > On 6 March 2014 03:53, Douglas Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu> > > > <mailto:gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: > > > > > > > > > On 3/5/14 5:25 PM, Tudor Popescu wrote: > > >> Hello, I have some questions on doing group comparisons with > > >> thickness, area and volume. Many thanks in advance for any help! > > >> > > >> 1) For a DOSS design with group and gender as categorical > > >> factors, I see that an interaction contrast ("Is there a > > >> group-gender interaction in the mean thickness?") still > > >> exists - but what does this contrast mean, given that DOSS by > > >> definition doesn't allow for interactions? > > > Are you using QDEC? If so, don't use the DOSS as the contrasts > > > are incorrect. It is possible to have an interaction among the > > > categorical factors with a DOSS. > > > > > >> > > >> 2) it makes sense that measures such as thickness are > > >> analysed vertex-wise in QDEC, however what does it mean when > > >> the dependent variable is area or volume - measures that do > > >> not make physical sense for a single vertex but only at the > > >> level of a region consisting of *several* vertices? > > > The interpretation is a little more difficult. Each vertex is > > > assigned an area equal to the average of the triangles > > > adjacent to it. This is just a value that can be mapped to a > > > common space like any other value (eg, thickness) (but there > > > is a special jacobain correction to account for stretching or > > > compression). Smoothing reduces the effect of having different > > > sized triangles. One can think of it like this: in the common > > > space (fsaverage) image having a patch of a certain size. When > > > you mapped that patch back to each individual, how big would > > > that patch be? You could then do group statistics on that > > > number. In this way you could analyze the entire hemisphere. > > > Now imagine doing this but making the patch smaller and smaller. > > >> > > >> 3) For values extracted from atlas regions with > > >> aparcstats2table, it seems that the product of the extracted > > >> CT and area is in the same order of magnitude as the > > >> extracted volume, but never really the same or even close - > > >> why, when the volume of a region should theoretically be the > > >> product of its surface area by its thickness? > > > It is an issue of how it is computed. Sum(CT*Area) != > > > Sum(CT)*Sum(Area). When computing volume, CT*Area is computed > > > for each vertex then summed across vertices. > > > doug > > > > > >> > > >> Tudor > > >> > > >> > > >> _______________________________________________ > > >> Freesurfer mailing list > > >> Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > <mailto:Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > The information in this e-mail is intended only for the person > > > to whom it is > > > addressed. If you believe this e-mail was sent to you in error > > > and the e-mail > > > contains patient information, please contact the Partners > > > Compliance HelpLine at > > > http://www.partners.org/complianceline . If the e-mail was > > > sent to you in error > > > but does not contain patient information, please contact the > > > sender and properly > > > dispose of the e-mail. > > > > > > > > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: > Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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