Hi Rick,
> Censoring outliers is done in afni_proc.py using the -censor_outliers option.
I have done this. I used the output of 3dvolreg to make a censor file.
> But if it is just one part of the brain that shows the outliers,
My question is: Is volreg able determine misalignments in part of the brain? That's what my "diff map" is showing.
> what would you want to do?
Perhaps I can use the the mean values across the entie "diff map" at each volume to determine if that TR has a neighboring, mis-aligned parital volume. I can create a censor motion file for these volumes and one or perhaps two volumes on either side.
Essentially, I want to create a censor file to use with -censor_outliers, but create that file from scanning for partial volume mis-alignments.
I think it's possible, but would be a waste of time if volreg is picking up this kind of partial volume mis-alignment.
Thanks, Peter
