Dear Karl,

I am a little bit confused with resting-state, stimulation, group and
number of scans but can I summarise that there is a within-subject
factor with N levels (A, B, C, etc) and each subject might or might not
have data for each of the levels? This would mean that you have up to N
contrast images per subject. If so, you can use a one-way ANOVA within
subject at the second level: for each subject, you select the
corresponding contrast images in "Scans" and for the "conditions" entry,
you would enter, e.g., 1:5 for a subject having data for all 5 levels,
or [1 2 4 5] for a subject with only four conditions with C missing.

Best regards,
Guillaume.


On 10/06/2021 21:22, Karl Lerud wrote:
> Hello all. I have a fairly simple resting-state BOLD analysis that I am doing, where the contrast at the first-level analysis is just a type of stimulation being off or on, let's call these OFF and ON, which alternates several times over the course of each scan. There are several types of this stimulation, which is the group distinction, let's call them A, B, C, D, etc., that I use for second-level group analysis. There are 100 scans in total, comprising the total of A, B, C, etc.
> 
> My problem is that I have far fewer than 100 subjects, because many of them contributed multiple scans. Some only contributed one, some may have contributed two to A and one to B, some may have contributed three to C but none to any other condition, etc. How many scans and which conditions they were vary widely subject to subject. 
> 
> So this sounds like it needs a mixed effects analysis, with subject coded as a random effect, correct? Is this simple to do in SPM's second level? I found a brief section on this topic in the manual, but I think it says everything needs to be equally distributed, the same number of scans per subject and subject per condition etc., in which case I am presumably out of luck. Also this section only mentions the GUI, and I have this all batch-scripted, so I would prefer to keep it that way. Is there something in my second-level model specification script where I can specify a mixed model, and then specify which scans came from which subjects? Thanks a lot, 
> 
> Karl
> 

-- 
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG