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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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.
OK, thanks! Francesco
On 17 March 2014 17:50, Douglas N Greve greve@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 <greve@nmr.mgh.harvard.edumailto: greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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.eduhttps://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 greve@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@nmr.mgh.harvard.edu
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Francesco Puccettone