3dDespike -ignore 0 -nomask -prefix despiked_dataset slicetimed_realigned_dataset+orig
- The "-ignore" option allows you to ignore the first "X" number of timepoints within a dataset. I
have never had a reason to ignore any of them, so I perform the command on all of my timepoints.
- The "-nomask" option tells 3dDespike to perform its magic on all of your voxels. Likewise, there is
also a command if you just want to perform 3dDespike on a specific ROI or mask, but I've never used it
before, so I'll refer you to the linux prompt 3dDespike help menu.
- As always the "-prefix" command allows you to determine the name of the output dataset.
- Remember to put in the input dataset as your last subcommand in the 3dDespike string. Also, the makers of Afni highly recommend that you use 3dDespike only after you've realigned your data.