On 06/11/2018 11:07 PM, Hua, Jessica wrote:
>
>
> Dear Freesurfer Experts:
>
>
> I analyzed my data following the guidelines on the FSL Tutorial/Group
> Analysis page . I am trying to plot the adjusted values (covariates:
> age, sex, and ICV) for the significant clusters for each of my
> participants.
>
I assume you mean FreeSurfer, not FSL?
>
>
> I set up the contrast to test group differences. So testing whether
> there is a difference between groups regressing out the effects of
> sex, age, and ICV. Contrasts created were [1 -1 0 0 0 0 0 0] and [-1
> 1 0 0 0 0 0 0].
>
>
> I then extracted values from this file
> (cache.th20.abs.sig.y.ocn.dat; i.e., the average value of each subject
> in each cluster) into my dataset. I believe these are the unadjusted
> values, correct?
>
These are the average thickness data (assuming you are using thickness
as input --y)
>
> I calculated total volume and total surface area by multiplying these
> values by the total number of vertices in each cluster.
>
Not sure what you mean here or how it works.
>
> To adjust for covariates, I ran a regression with the
> ExtractedClusterValues as the DV and Group, Sex, Age, and ICV as
> predictors. Looking at the output, there was no significant effect of
> group (p = .769; whereas in FreeSurfer the cluster-wise p < .001).
>
What were you using to do this test? You really need to have exactly the
same design matrix and contrast matrix.
>
> Also when I plotted the predicted values adjusting for covariates, the
> means between the groups were very similar.
>
>
> Why am I getting a p = .769 when I adjust for covariates, but
> FreeSurfer has a cluster-wise p < .001? Or is there a way to calculate
> adjusted values in FreeSurfer?
>
>
> Best,
>
>
> Jessica
>
>
>
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