I noticed the 3dmaskave collapses all of my ROIs into one output. I managed to suppress this by using the -mrange a b flag and defining a and b as the sub brick of interest. I was wondering if there is a direct way to calculate all the means for each ROI (just like 3dROIstats does) and then graph the corresponding ROI mean in each sub-brick over the time course.

For example, if 3dROIstats prints out

sub-brick Mean_1 Mean_2 Mean_3
0 3000 2900 2950
1 2960 3000 3100
2 2890 3120 2981

Then i want to graph everything in the column Mean_1, then in Mean_2 and so on, against the number of time points (on x-axis). Using 3dmaskave, I think i will need a shell script to loop through all the sub-bricks. Is there a way to do it directly, or should I start writing my script?

-Matt