OK, thanks! Francesco
On 17 March 2014 17:50, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > Hi Francesco, please remember to post to the list. Thanks! The baseline is > a regressor with all ones, so it is measured throughout the scan, not just > during the rests. This makes the other regression coefficients relative to > baseline. > > doug > > > On 03/17/2014 01:05 PM, Francesco Puccettone wrote: > >> thank you Doug, I am just still not sure about comparing to the baseline >> vs comparing between conditions; since the baseline it's not one of the >> predictors, how is it exactly used to define the contrasts and influence >> the regression coefficients? >> >> And is it the case that the "baseline" is taken as the average of all >> non-stimulus (rest) periods in the scan, i.e. the "zero" periods in the >> block-design boxcar diagram? >> >> Thank you again, >> --Francesco >> >> >> On 17 March 2014 15:33, Douglas N Greve <gr...@nmr.mgh.harvard.edu<mailto: >> gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> On 03/15/2014 06:35 PM, Francesco Puccettone wrote: >> > Dear Freesurfer community: >> > >> > I have some (perhaps silly, but I think fundamental) questions about >> > contrasts in functional analyses: >> > >> > >> > 1. When wanting to see what regions are activated by exposure to a >> > certain stimulus (blocked-design), what is the exact stats that is >> > happening voxel-wise: >> > >> > (i) correlation between the time series of the HRF-convoluted >> BOLD and >> > that of the behavioural stimulus that was used, or >> > (ii) t-test between the BOLD signal during the stimulus and the BOLD >> > signal during a resting baseline >> > >> > If ii) is the answer, then is "baseline" taken as an average of all >> > non-stimulus (rest) periods in the scan, i.e. the "zero" periods in >> > the block-design boxcar diagram? >> Neither. A GLM is set up with regressors for you conditions and >> nuisance >> variables. The GLM is fit to the time course to compute a regression >> coefficient for each regressor. This is a multivariate operation and >> does not reduce to a simple correlation. For a task regressor, the >> regression coefficient indicates the amplitude of the HRF. This >> amplitude is tested with a t-test >> > >> > >> > >> > 2. When wanting, on the other hand, to see what regions are >> active in >> > condition A but not in condition B (so a comparison this time), >> is it >> > the case that i) is no longer a choice and a t-test always has to be >> > used between condition A and condition B? If so, is the >> > stimulus-vs-baseline situation from the previous question just a >> > special case of this, where condition B = (passive) baseline? >> This would be a conjunction analysis that does not reduce to a simple >> contrast. >> > >> > >> > >> > 3. Is it the case that a contrast probing the difference between two >> > groups is using independent samples t-tests, whereas one probing the >> > within-subject difference between two time-points is using >> > paired-samples t-tests? >> Between groups is independent two-sample. Within subject uses a >> GLM and >> does not reduce to a simple paired formula (but that is basically the >> right way to think about it) >> doug >> > >> > >> > Thank you for your help:-) >> > >> > --Francesco >> > >> > >> > _______________________________________________ >> > 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 <tel:617-724-2358> >> Fax: 617-726-7422 <tel: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 >> >> >> 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. >> >> >> > -- > 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/ > >
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