Dear Doug,

Thank you very much for your response.

>> (1) why did I get Frame (0-8) for my data that should have 12 frames?

> When you use -rmprestim, it subtracts the mean of the prestim baseline

> AND removes the prestim time points (-4 -2 and 0) so you only end up

> with 9 frames.

I see. This makes perfect sense.

>> (2) how can I visualize contrasts created with -setwdelay?

> Your visualization command is correct. I don’t understand why you are

> seeing the same image for each frame. Can you load them separately and

> see if they are different?

I tried to load them separately, but still got the same images.

tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w1_all_null -map sig

tksurfer-sess -df sessdirfile -s YY03 -analysis YY.sm5.lh -contrast w5_all_null -map sig

I also loaded /YY03/bold/YY.sm5.lh/w1_all_null/sig.nii.gz, and /YY03/bold/YY.sm5.lh/w5_all_null/sig.nii.gz, using GUI on FreeView, still got the same images.

Then, I created new contrasts without -rmprestim

mkcontrast-sess -analysis YY.sm5.lh -contrast w1b_all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -setwdelay [1 0 0 0 0 0 0 0 0 0 0 0]

mkcontrast-sess -analysis YY.sm5.lh -contrast w5b_all_null -a 1 -a 2 -a 3 -a 4 -a 5 -a 6 -a 7 -a 8 -c 0 -setwdelay [0 0 0 0 1 0 0 0 0 0 0 0]

Without -rmprestim, I was able to see different maps.

So it looks like when I used -rmprestim, I failed to create different sig.nii.gz files for the different contrasts.

Now, I can continue my analyses without -rmprestim. But I have one follow up question.

(3) when I used -rmprestim with mkcontrast-sess, is it correct to assume that the statistical results produced by selxavg3-sess were based on the data with the prestimulus activation subtracted?

With -rmprestim, sig.nii.gz had 9 frames. I am confused because, the data I visualized with freesurfer version 5 by clicking the activated areas had 12 frames. I am wondering where did the first three frames came from in those plots.

Thank you in advance.

Shogo