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  

|
March 03, 2020 04:15PM
Hi Rick! Ah that's good =).

1) I think it's the align part since it says "+ * Enter alignment setup routine" a few rows over the errors. It seems like the automatic review part (reading the cost file) fails since it prints the same cost for boths flips which I guess are the default or starting costs of 1000. I'll email you the full output but it should also be in the output we allready uploaded. I also think Paul Taylor was investigating this.

The other questions probably popped up due to me assuming that EXACTLY these settings were recommended for task-processing. E.g. that you saw through optimizaiton that despiking was not optimal to use for task. But I now see that this is not the case =). Thanks! I'll just comment on the anaticor part anyway:

In an older post of mine I vaguely someone saying that anaticor_fast was just as good and faster and now the recommended option. So I was just curious to why the 6b script (which only produces anaticored stats) did not use it. But perhaps this it nitpicking. With a newer scanner (Siemens 3T prisma) would we expect ANATICOR to help that much? ANATICOR corrects for spatial drift in the coil-sensitivity, right? So far we see no "improvement" in the group stats allthough I acknowledge that weaker clusters could be more "true" than stronger clusters ;).

I get the main point, despiking won't hurt. Neither wont "deriv" motion (apart from losing DOF). It would be awesome though if you could check the flip-errors we get!

Thanks a bunch!!
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