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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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Thanks, Gang, that does explain it well. I appreciate your help with this!
-Dominic
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dsf215
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AFNI Message Board
Hi Gang,
Thanks so much for the info. Follow-up question--why is it better to center outside of AFNI for this analysis as opposed to centering within AFNI?
-Dominic
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dsf215
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AFNI Message Board
Hello,
I am analyzing a between groups dataset (2 groups) using 3dttest++, and I have what I hope is a quick question regarding setting up the analysis.
I would like to look at a 3-way interaction at the whole brain level of group x age x anxiety scores. If I set up the analysis with setA being one group (e.g., control) and setB being the other group (e.g., experimental), and put into my
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dsf215
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AFNI Message Board
Hi Rick,
Thanks for your reply to this, and sorry it took me so long to write back; I was out of the country for a bit after I sent my initial inquiry.
Your initial thought was correct, creating stimulus timing files for this particular project is going to be quite involved and I would like to not have to do it needlessly for subjects that will have to be thrown out anyway. I believe that
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dsf215
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AFNI Message Board
Hi Afni experts,
I have what may prove to be a stupid question, but I am going to ask it anyway.
I know that in the documentation for afni_proc.py it states that the script will always perform the tcat block. However, is there anyway at all in which one could circumvent this?
The reason I ask is as follows. I would like to run all preprocessing steps first before running the single s
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dsf215
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AFNI Message Board
Hi Rick,
Thanks for the clarification. Very much appreciated.
-Dominic
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dsf215
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AFNI Message Board
Hi Rick,
Thanks for your quick reply. I checked our version of afni and it appears to be the most updated (AFNI_2011_12_21_1014), though if that is incorrect please let me know.
I am pasting below the relevant info from one subject's out.ss_review file. Could you just point me to which would be the average value calculated with censored TRs excluded, or alternatively, if that infor
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dsf215
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AFNI Message Board
Hello,
I have a quick question regarding the output.proc file that is created when running afni_proc.py. In the output.proc text file, am I correct in assuming that the line that notes 'average motion (per TR)' is essentially a measure of mean framewise displacement, and if so, is this value calculated including or excluding any volumes which are censored?
Thanks so much,
Domini
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dsf215
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AFNI Message Board
Hello,
I have what is hopefully a quick question regarding resting state analyses in AFNI. If one were to use 3dBandpass to bandpass nuisance regressors (e.g., motion, CSF, global signal) with the -ort option, are the nuisance regressors essentially being regressed out after being bandpassed?
Thanks,
Dominic
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dsf215
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AFNI Message Board
Hi Gang,
Thank you for confirming re: SPMG2/3/GAM.
I have one other question (for now). When creating stimulus timing files for an event-related task designed as I noted in the first message in this thread, how does AFNI know how long each stimulus should be modeled for if only the onsets are required for the stimulus timing files when using something like SPMG2 or GAM? In other words,
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dsf215
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AFNI Message Board
Hi Gang
Thank you for your quick reply and for the suggestions. You are correct, I would want to model both phases of the task, decision and outcome. I have never used a model-free approach as per your suggestion, but I will certainly look into using TENT or CSPLIN as it sounds like that could be a fruitful approach. If I wanted to compare that, however, to a standard double gamma HRF would
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dsf215
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AFNI Message Board
Hi AFNI users,
I am relatively new to AFNI (though not to neuroimaging), and I am wondering if someone might be able to provide some suggestions on the best response model to employ to analyze an event-related task. This is a relatively simple reward-learning task in which the timing structure is as follows:
Decision (2s)
ISI (1-4s)
Outcome (2s)
ITI (4-6s)
I was hoping to simply appl
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dsf215
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AFNI Message Board