Hi Dana,

Have you considered an F-test [1 0 0 0 ...; 0 1 0 0 ...]? Maybe there is a reasonable response with negative, but not with neutral (or vice versa), and averaging both may not reveal anything then.

That said, regarding the last scans, it isn't a big problem. I think you're talking about a few volumes only. It shouldn't be an issue to have runs with different lengths.

All the best,


On 29 October 2015 at 23:22, Dana Wagshal <[log in to unmask]> wrote:
Hi FSL group,

I have a declarative memory Encoding task where I ask subjects if the picture they see is negative or neutral. Right after each picture I have a jittered fixation cross. I have set up my first-level GLM with EV1 = Negative pictures, EV2 = Neutral pictures, EV3-8 = motion regressors, and EV9 = missed trials. I wanted to know what brain regions were involved in the task, (task-everything else), and I used a contrast of (1 1). But in looking at the results, I expected more activation.

I looking back at my task, I realized that all the subjects finished the task early and had to wait until the scan was done. A lot of time, subjects were done with the task for over 1 minute. So there are quite a few TRs at the end of the scan that have nothing to do with my task. I assume this is the reason why I didn't get as much activation as expected, due to mind wandering etc. Sorry for the basic question, but is there a standard or acceptable method to deal with these TRs? What is typically done in event-related designs?

It seems like it would be ok to remove them, and if so, is there a systematic way of removing the TRs? For example, would I remove the TRs after 8 seconds or so had gone by from the last trial? In this way each subject would have a different task length but there wouldn't be a lot of time when the subject is mind wandering. Or would I find the slowest person and remove the same number of TRs from all subjects? With this method at least the task length would be the same, but then you would still have subjects that have TRs when they're just mind wandering.

Your help and insight would be greatly appreciated!!!