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

History of AFNI updates  

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February 07, 2020 12:47PM
Hi Rick,

Thank you very much for your reply!

> My guess is that you want srms, as it must be in [0,1]. But maybe there is a different scalar that you want, which would also
> scale into the 0.5 threshold. There is currently no method to apply this in afni_proc.py, as those curves seemed to noisy to
> be robust. But if it is something you feel is important, I could consider adding something.

Our initial idea was to do a censoring based on Power et al., 2012 and, particularly, based on intensity instead of the 6 motion parameters, and it would be interesting if AFNI had a way to do it (for example, censoring with dvars or srms), but using enorm is fine! I have also read here the explanations why it's more appropriate to use enorm than fd (it is a calculation more proportional to the real movement), and for now, we will apply enorm to censoring because it seems very reasonable.

> Regarding enorm (this time of the motion parameters), note that it is not generally used in the linear regression. The (de-meaned)
> motion parameters are used, and/or their derivatives. But enorm itself is generally just used for censoring and QC. Note that
> enorm would capture little that the motion derivatives would not.

It make sense!

> The dvars regressor could be used in the regression (though not currently via afni_proc.py). In that case, scaling would not matter much.
> Does that seem reasonable?

A doubt emerged related to this: Is it correct to use as a regressor a file that contains a value for each volume except for the first volume?
(Because the first value in the dvars file is always 0.)

Thanks again!

Best wishes,
Marina.
Subject Author Posted

enorm and dvars

Marina Fernandez Alvarez February 07, 2020 06:24AM

Re: enorm and dvars

rick reynolds February 07, 2020 09:43AM

Re: enorm and dvars

Marina Fernandez Alvarez February 07, 2020 12:47PM

Re: enorm and dvars

rick reynolds February 07, 2020 01:02PM

Re: enorm and dvars

Marina Fernandez Alvarez February 10, 2020 03:47AM