3dDespike custom options using afni_proc.py


When using -despike_opts_3dDes to pass NEW25 (so as to choose the NEW25 algorithm), the afni_proc.py generated script does not overwrite NEW with NEW25 (i.e., the generated proc script contains 3dDespike -NEW -NEW25).
Please advise.

Thank you,

Hi Ankit,

I did not realize there was something newer than plain old NEW…

Anyway, a good thing to keep in mind regarding afni_proc.py options in general is that the -A_B_opts options are specifically for options for processing block A, program B that afni_proc.py does not know about (and keep track of). Since afni_proc.py does keep track of -NEW, using -despike_pts_3dDes is not appropriate.

However, at the moment, you can cheat and use what you are doing, PLUS “-despike_new no”, to tell it not to add the -NEW option.

But I will modify -despike_new to include NEW25 as one of the parameters, making yes, no, NEW, NEW25 all valid (where yes would mean the default of NEW). That will be available next time we build, assuming don’t get distracted before the build (which NEVER happens… :).

How does that seem?

  • rick

Ah, I see! Thanks for pointing it out. No rush, its a small thing and I was confused why it was doing that.

Thanks for your time!