I’m having some issues with determining maximum motion displacement before and after censoring using 1d_tool’s -show_max_displace option. For example, with one of my subjects, the maximum motion displacement value only changes after censoring if I set the Euclidean norm cut-off (-censor_motion) at 0.7 or lower. If I use 0.8 or higher, the maximum motion displacement value does not change with censoring, even if there is a TR omitted for excess motion in the censor file.
Why is this? I would think the maximum motion displacement would change, regardless of the cut-off, as long as there is at least one TR that is being censored. The maximum motion displacement for the next highest TR would be reported instead. I would suspect the TRs listed in the censor file are not being censored in the dfile, but then why would it work at some cut-off values and not others? That, and the script matches the example in the help for 1d_tool. I’ve copy/pasted the relevant script below:
#Determine maximum motion displacement (mm) before censoring
1d_tool.py -infile dfile.breathhold.E.1D -show_max_displace
#Create a file that will allow us to censor TRs where the Euclidean norm of the motion parameter derivative is more than 0.3 (~mm/degrees). This is a good value for healthy adults, but I may need to increase this cut-off depending on the number of TRs that are being censored.
1d_tool.py -infile dfile.breathhold.E.1D -set_nruns 1 -set_tr 4 -censor_motion 0.8 motion.105.breathhold.E
#Display a list of the TRs censored based on motion, and the total number of censored TRs.
1d_tool.py -infile motion.105.breathhold.E_censor.1D -show_censor_count -show_trs_censored comma
#Determine maximum motion displacement with censoring
1d_tool.py -infile dfile.breathhold.E.1D -show_max_displace -censor_infile motion.105.breathhold.E_censor.1D