Re: [Freesurfer] fMRI contrasts in Freesurfer

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
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
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