Alternative fMRI analysis - single session data?

[gt235]

I have data from a slightly odd design.

There are 3 conditions (rest, stimulus and post-stim) reapeated 3 times for 3 different stimuli (all repeated measures). As it is not a block design (only 20 scans per condition/repeat) I can't use SPM?. I have extracted ROI data using MarsBar templates into excel (Trans and rotation paramaters and ROI signal).

I would first like to compare ROI signal between the 3 repeats for each individual (using trans and rotation parameters, plus other variables, as covariates). Then further analysis on the 'pure' signal across groups.

Does anyone have any suggestions on the stats and software to compute this? I am thinking a regression model for the covariates and individual analysis, however could it be too simplistic and time consuming. The problem is only having one 'block' of data per condition.

Any help would be greatly apprieciated.