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help > RE: Questions about setup & within subject design
Mar 8, 2012 04:03 AM | Alfonso Nieto-Castanon - Boston University
RE: Questions about setup & within subject design
Hi Darren,
I would leave the 'pre' and 'post' main effects in step (1) (as part of the potential confounds list), this simply removes the average effect across each session (even though this is also done by the filtering step) but it also helps correct any small transient effects at the beginning of the session should these exist in your data. If pre and post main effects are included as confounds they will then not appear in step (2) (as part of the potential sources list), where you are right that typically you would not need to add these as sources.
Just for reference, the toolbox will offer as potential 'sources' any ROI timeseries, first-level covariate timeseries, or condition main effect timeseries that has not been used already in the previous preprocessing step (those effects used as confounds are effectively removed from the data so there is no point in including these later on). In the typical scenario you will only include in the 'sources' list those ROIs that you wish to use either for seed-to-voxel, ROI-to-ROI, or graph-theory analyses. We only added in a recent version the ability to also include first-level covariates and task-related timeseries as additional 'sources' for thoses cases where people wished to define more complex first-level models beyond the standard bivariate correlation models.
Best
Alfonso
Originally posted by Darren Gitelman:
I would leave the 'pre' and 'post' main effects in step (1) (as part of the potential confounds list), this simply removes the average effect across each session (even though this is also done by the filtering step) but it also helps correct any small transient effects at the beginning of the session should these exist in your data. If pre and post main effects are included as confounds they will then not appear in step (2) (as part of the potential sources list), where you are right that typically you would not need to add these as sources.
Just for reference, the toolbox will offer as potential 'sources' any ROI timeseries, first-level covariate timeseries, or condition main effect timeseries that has not been used already in the previous preprocessing step (those effects used as confounds are effectively removed from the data so there is no point in including these later on). In the typical scenario you will only include in the 'sources' list those ROIs that you wish to use either for seed-to-voxel, ROI-to-ROI, or graph-theory analyses. We only added in a recent version the ability to also include first-level covariates and task-related timeseries as additional 'sources' for thoses cases where people wished to define more complex first-level models beyond the standard bivariate correlation models.
Best
Alfonso
Originally posted by Darren Gitelman:
Alfonso,
That was very helpful. I have a couple other questions.
I set up the conditions as you suggested: pre and post. Pre had values of onset=0, duration=490 for session 1 and was empty for session 2, and vice versa for post.
1) On the preprocessing screen, Conn adds the pre and post conditions to the confound list. Does this make sense or should I remove them as confounds?
2) On the First-level results screen, Conn adds pre and post to the sources. I think they should also be removed from here as well. Is that correct?
Thanks,
Darren
That was very helpful. I have a couple other questions.
I set up the conditions as you suggested: pre and post. Pre had values of onset=0, duration=490 for session 1 and was empty for session 2, and vice versa for post.
1) On the preprocessing screen, Conn adds the pre and post conditions to the confound list. Does this make sense or should I remove them as confounds?
2) On the First-level results screen, Conn adds pre and post to the sources. I think they should also be removed from here as well. Is that correct?
Thanks,
Darren
Threaded View
| Title | Author | Date |
|---|---|---|
| Darren Gitelman | Mar 7, 2012 | |
| Tamara Sussman | Feb 23, 2018 | |
| Aisling O'Neill | Feb 14, 2019 | |
| Alfonso Nieto-Castanon | Feb 14, 2019 | |
| Aisling O'Neill | Feb 14, 2019 | |
| Alfonso Nieto-Castanon | Mar 7, 2012 | |
| Darren Gitelman | Mar 7, 2012 | |
| Alfonso Nieto-Castanon | Mar 8, 2012 | |