> This has resulted in 4 sw*.nii files for each subject.
If you only have three volumes for some of the subjects then you should also have only three c1 files, three wc1 files, ...
> 2) can I perform either a paired sample t-test or GLM (flex factorial) using the final output sw*.nii files, to for example, look
> at changes in gray matter across time?
As you have only one factor (time) you would simply use a "One-way ANOVA - within subject". Alternatively you can also run several "paired t-tests" to compare e.g. time 1 and 2. "Flexible factorial" is possible as well, but if you specify everything correctly it's identical to the "One-way ANOVA - within subject". However, within SPM you can only compare those subjects for whom data is available for all the investigated time points. There's no option for missing data/empty cells.
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