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 21, 2020 08:23AM
Great, thanks!

I looked and the unflipped was indeed better. But would be really nice if you could check if there is a bug or implementation fault from my side!

I also noticed that in the suggested proc blurring was used with a 4 mm setting. We kind of have a debate here regarding blurring/smoothing.

In a sense the data is already blurred biologically, MR scanning and then normalization. And another thing is that in AFNI we correct for false positives via FWHMx+clustsim where spatial smoothness/autocorrelation is measured and converted into tables of p-values vs cluster-sizes. If we use blur we usually get stronger stats and perhaps bigger clusters but we are then penalized with more conservative clust-tables since we have introduced smoothness. Is it a net gain using blur compared to penalty we get in the per-voxel p-value vs cluster size in the clust tables (clustsim output)?

Since blurring is in the current recommended afni-proc example. (I know this is a difficult question and might be per case basis and depend on the task and MR resolution at hand -but generally...).
Subject Author Posted

Updated AFNI pre-proc pipeline

Robin February 21, 2020 06:51AM

Re: Updated AFNI pre-proc pipeline

ptaylor February 21, 2020 07:17AM

Re: Updated AFNI pre-proc pipeline

Robin February 21, 2020 08:23AM

Re: Updated AFNI pre-proc pipeline

ptaylor February 21, 2020 08:42AM

Re: Updated AFNI pre-proc pipeline

Robin February 21, 2020 08:57AM

Re: Updated AFNI pre-proc pipeline

Robin February 21, 2020 09:24AM

Re: Updated AFNI pre-proc pipeline

ptaylor February 21, 2020 09:35AM

Re: Updated AFNI pre-proc pipeline Attachments

Robin February 24, 2020 04:53AM

Re: Updated AFNI pre-proc pipeline

ptaylor February 24, 2020 07:43AM

Re: Updated AFNI pre-proc pipeline

Robin February 24, 2020 07:59AM

Re: Updated AFNI pre-proc pipeline

Robin March 02, 2020 03:02AM

Re: Updated AFNI pre-proc pipeline

rick reynolds March 03, 2020 09:51AM

Re: Updated AFNI pre-proc pipeline

Robin March 03, 2020 04:15PM

Re: Updated AFNI pre-proc pipeline

krisknut March 11, 2020 02:35PM

Re: Updated AFNI pre-proc pipeline

rick reynolds March 11, 2020 04:35PM