3D Despike

  • Purpose: Removes "spikes" from your 3D dataset and replaces it with something better. I haven't used

    SPM for a while but I think this is similar to the globalvariate option in the ROI's toolbox. There is a good explanation of why you should use the 3dDespike command on the Afni website: http://afni.nimh.nih.gov/afni/

  • Usage: Below is an example for 3dDespike.
           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.