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help > RE: How to define "site" as covariate
Mar 10, 2022 01:03 AM | Alfonso Nieto-Castanon - Boston University
RE: How to define "site" as covariate
Hi Nancy,
Yes, unfortunately the warning correctly indicates that you cannot possibly control for site-effects if those are exactly co-linear with your group-effects (e.g. as in your case if all group A subjects came from site A and all group B subjects came from site B). When looking at group-effects while controlling for site-effects the analyses will effectively perform this control by estimating the differences in connectivity between the two groups when compared separately within each site (e.g. groupA - groupB differences restricted to only subjects from site1, groupA - groupB differences from subjects in site2, etc.), so the warning is just indicating that unfortunately those comparisons simply cannot be made in your case.
Best
Alfonso
Originally posted by Nancy Mugisha:
Yes, unfortunately the warning correctly indicates that you cannot possibly control for site-effects if those are exactly co-linear with your group-effects (e.g. as in your case if all group A subjects came from site A and all group B subjects came from site B). When looking at group-effects while controlling for site-effects the analyses will effectively perform this control by estimating the differences in connectivity between the two groups when compared separately within each site (e.g. groupA - groupB differences restricted to only subjects from site1, groupA - groupB differences from subjects in site2, etc.), so the warning is just indicating that unfortunately those comparisons simply cannot be made in your case.
Best
Alfonso
Originally posted by Nancy Mugisha:
Hi
Alfonso,
I have a peculiar case trying to control for site for two groups. All subjects in group A came from site A and all subjects in group B came from site B. i want to do a -1 1 contrast to look at differences between groups.
When I do option 3) mentioned in your post do do this between group contrast, I get a "Warning" (see screenshot: possible incorrect model, non-estimable contrast. suggestion simplify second-level model). What can I do to go around this or if there is another way I can control for site difference.
Thank you so much,
Nancy
Originally posted by Alfonso Nieto-Castanon:
I have a peculiar case trying to control for site for two groups. All subjects in group A came from site A and all subjects in group B came from site B. i want to do a -1 1 contrast to look at differences between groups.
When I do option 3) mentioned in your post do do this between group contrast, I get a "Warning" (see screenshot: possible incorrect model, non-estimable contrast. suggestion simplify second-level model). What can I do to go around this or if there is another way I can control for site difference.
Thank you so much,
Nancy
Originally posted by Alfonso Nieto-Castanon:
Hi Till,
Exactly, simply define a set of site-specific covariates (e.g. SITE_1, SITE_2, etc.) and include these as covariates-of-no-interest in your second-level analysis (e.g. image attached).
For example, if you have three sites and have already imported a 2nd-level SITE covariate with values 1 to 3 indicating the site of each subject, you could:
1) discretize that variable: in the Setup.Covariates.2nd-level tab select your covariate SITE, and then click on 'Covariate tools. Discretize selected covariate'. That will create three new covariates named SITE_1, SITE_2 and SITE_3
2) (optionally / rarely-necessary) center those new site-specific covariates to your desired control-level (e.g. average across all subjects): in the same tab select jointly SITE_1, SITE_2 and SITE_3, then click on 'Covariate tools. Orthogonalize selected covariates', and select the variable 'AllSubjects' as your only orthogonal factor
3) add those site-covariates as controls in your second-level analysis. For example, in the Results (2nd-level) tab, after defining your desired analysis (e.g. a two-sample t-test comparing PLACEBO and TREATMENT subjects), simply select the option that reads 'add/remove SITE_1 as control covariate' (and repeat for SITE_2 and SITE_3). You should be seeing something like in the example attached, which will estimate the differences between groups while controlling for site effects.
Hope this helps
Alfonso
Originally posted by Till Langhammer:
Exactly, simply define a set of site-specific covariates (e.g. SITE_1, SITE_2, etc.) and include these as covariates-of-no-interest in your second-level analysis (e.g. image attached).
For example, if you have three sites and have already imported a 2nd-level SITE covariate with values 1 to 3 indicating the site of each subject, you could:
1) discretize that variable: in the Setup.Covariates.2nd-level tab select your covariate SITE, and then click on 'Covariate tools. Discretize selected covariate'. That will create three new covariates named SITE_1, SITE_2 and SITE_3
2) (optionally / rarely-necessary) center those new site-specific covariates to your desired control-level (e.g. average across all subjects): in the same tab select jointly SITE_1, SITE_2 and SITE_3, then click on 'Covariate tools. Orthogonalize selected covariates', and select the variable 'AllSubjects' as your only orthogonal factor
3) add those site-covariates as controls in your second-level analysis. For example, in the Results (2nd-level) tab, after defining your desired analysis (e.g. a two-sample t-test comparing PLACEBO and TREATMENT subjects), simply select the option that reads 'add/remove SITE_1 as control covariate' (and repeat for SITE_2 and SITE_3). You should be seeing something like in the example attached, which will estimate the differences between groups while controlling for site effects.
Hope this helps
Alfonso
Originally posted by Till Langhammer:
Originally posted by Zahra Mor:
Hey People!
I have the same problem!!!!
Anybody found a solution?
best wishes
Till
Dear Ali, conn users and experts,
I wonder if you have found an answer to your question regarding how to correct the multi site (scanner) effect, probably through defining a categorical second level covariate?
Thanks in advance!
I wonder if you have found an answer to your question regarding how to correct the multi site (scanner) effect, probably through defining a categorical second level covariate?
Thanks in advance!
Hey People!
I have the same problem!!!!
Anybody found a solution?
best wishes
Till
Threaded View
| Title | Author | Date |
|---|---|---|
| Julia Werhahn | Nov 6, 2017 | |
| Julia Werhahn | Nov 8, 2017 | |
| Ali Amad | Dec 14, 2017 | |
| Zahra Moradimanesh | Oct 31, 2020 | |
| Till Langhammer | Jan 18, 2021 | |
| Alfonso Nieto-Castanon | Jan 18, 2021 | |
| max345 | Jul 5, 2023 | |
| Alfonso Nieto-Castanon | Jul 5, 2023 | |
| Alex G | Dec 7, 2022 | |
| Alfonso Nieto-Castanon | Dec 23, 2022 | |
| Nancy Mugisha | Mar 2, 2022 | |
| Alfonso Nieto-Castanon | Mar 10, 2022 | |
| Dilip Kumar | Jun 25, 2021 | |
| Victoria Okuneye | Jun 27, 2018 | |
| Ekaterina Pechenkova | Nov 8, 2017 | |
| Ekaterina Pechenkova | Nov 6, 2017 | |