After deciding on a cutoff for an outlier volume, you can use 1deval to determine if it's over threshold and write a 1D file for each run (1's are keep that TR, 0's are censor them). Concatenate those files (e.g. cat). Then put them into 3dDeconvolve using the "-censor" flag.

If you wanted to use afni_proc.py with dmBLOCK, you can use sed to do a quick replacement of "stim_times" with "stim_times_AMX" after generating the afni_proc.py script. I've included the MacOS X friendly syntax for SED below.

sed -i '' 's/-stim_times/-stim_times_AM1/g' afni_procOutputScript.tcsh

My workflow generates the afni_proc.py script, runs this sed command and then executes the script.



Edited 1 time(s). Last edit at 06/21/2012 08:25PM by Peter Molfese.