Hi Rick,
Thanks for the help. One final question. In my analysis I perform all of my steps in subject space (including creating correlation files from my target seed). I then warp my correlation maps to MNI space. For 3dClustSim would it make sense to calculate my individual ACF parameters for each subject in subject space, determine the average of all subjects, and still provide my MNI mask for the 3dClustSim analysis. My thoughts are that since the pb04 file and analysis is in subject space (and I have full_mask per subject), it may make sense to use these estimates of the noise smoothness. However, I would still supply my MNI mask as the mask since I want to evaluate all voxels within the mask that are in MNI space. The other option is to warp all subjects to MNI and extract the smoothness based on the group mask used in 3dMVM. I just wasn't sure if it best to include warping in the nosie estimate when the values were calculated in subject space, or if the added smoothness is needed since residuals are "ideally" calculated from the stats residuals (similar to 3dttest++).
Thanks,
Ajay
Edited 1 time(s). Last edit at 08/15/2016 06:14PM by AjaySK.
