AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Daniel Glen
November 13, 2009 04:53PM
Sorry, I can't comment on the specific values that come out of 3dDespike; I don't have much experience with that program.

To look at any individual sub-brick, you can specify a sub-brick number in brackets like this:

3dBrickStat -count -non-zero spike+orig'[3]'

This will calculate a mean at the fourth sub-brick time point. You might do this in a loop over all sub-bricks, or you could use a program that would do this particular task for you like 3dROIstats or 3dmaskave. 3dTqual and 3dToutcount do give you the most likely bad TRs. Also just using the graph viewer in the AFNI GUI is a good way to quickly assess quality.
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Subject Author Posted

Despike

Michael Amlung November 09, 2009 01:20PM

Re: Despike

Daniel Glen November 09, 2009 02:29PM

Re: Despike

Michael Amlung November 09, 2009 02:53PM

Re: Despike

Daniel Glen November 09, 2009 05:29PM

Re: Despike

Michael Amlung November 09, 2009 08:54PM

Re: Despike

Michael November 13, 2009 03:48PM

Re: Despike

Michael November 13, 2009 03:55PM

Re: Despike

Daniel Glen November 13, 2009 04:53PM