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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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Results 1 - 30 of 53
Hello,
I am running amplitude modulation analyses with one AM (let's call it response). If I want to compare the modulation of response to condition 1 vs condition 2 on the group level (a contrast of condition1[1] - condition2[1] ) do I need to adjust the way the AM events on the individual level are being de-meaned? Specifically, since currently each AM event is being demeaned within eac
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MeganQ
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AFNI Message Board
Hi Gang,
One other quick question. If I remove the mean (across subjects for each condition) from each subject, will 3dLME then demean a second time while it's running? Thank you!
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MeganQ
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AFNI Message Board
Hi AFNI experts,
I'm running amplitude modulation analyses, but at the group level I just want the overall main effect (e.g., I have no contrasts or conditions). I have been unable to find any tutorials that go over setting up group level analyses without contrasts (probably because it's not common!). When I run it with the following script, not specifying any glt, I simply get the I
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MeganQ
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AFNI Message Board
Hi Rick,
Thank you very much! I will do so and see if that helps the output.
Best,
Megan
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MeganQ
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AFNI Message Board
Hello AFNI experts!
I have a perplexing problem. I have previously run amplitude modulation scripts (very very similar to the one I'll share below) and successfully got output for both the #0_coef as well as the #1_coef amplitude modulator. When I looked at the X.xmat.1D file I similarly correctly saw my standard regressor, then my demeaned AM regressor.
However, I re-ran a very simil
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MeganQ
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AFNI Message Board
Hi Gang,
Thank you, yes you understand it correctly! And it does correlate with reputation for some subjects. And just to clarify that be the overall mean aggression (e.g., take every subject's average aggression across conditions and use that to demean?).
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MeganQ
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AFNI Message Board
Hi Gang,
Hopefully what I have below is what you're asking for!
For reputation, there are three levels (Nice, Mean, Unpredictable) and for aggression, it is a continuous variable, but there will be a measurement for Nice, Mean and Unpredictable. So average aggression to Nice, average aggression to Mean, and average aggression to Unpredictable.
My effects of interest are brain respo
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MeganQ
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AFNI Message Board
Hello!
Hope your week is going well. I am trying to run a group level analysis where I have a within subjects variable (Reputation) and a between subjects variable (Aggression), but my between subjects variable also varies within subjects (Reputation). Essentially, I have different reputations (Mean, Nice, UnpMean, UnpNice) and there is an average aggression value for each of those (aggressio
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MeganQ
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AFNI Message Board
Hi Rick,
Thank you so much for the input! I'm going to digest this, and consult with my advisor. I'll let you know if I have any further questions after that. Thank you again!
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MeganQ
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AFNI Message Board
Hi AFNI experts,
I really appreciate all your help as I move through amplitude modulation in AFNI! I have successfully (yay!) run individual level analyses for my participants, and am looking at the output to ensure I both understand it and have done analyses correctly. For a little more context, I have pasted a portion of my AFNI proc script below and denoted which events are amplitude modula
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MeganQ
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AFNI Message Board
Hi Rick,
Thanks so much! Good to hear that a GOFORIT 4 is acceptable in this case.
Yes! I'm trying to do parametric (amplitude) modulation (with onset*behavior:duration). I would be ok using just the amplitude modulator (onset*behavior) and providing the duration in a BLOCK(1,duration) function if that's recommended (and in that case I would use AM1 correct, since I'd only ha
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MeganQ
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AFNI Message Board
Thank you so much! Please let me know what would be easiest for you. Happy to send in an email.
Here are those files:
class_agg.1D (not offset)
0.011:5
0.011:5
0.016:5
Mean_anticipation_agg.1D (not offset)
43.711*5:3.017 56.278*5:3.017 67.845*5:3.016 164.878*5:3.017 177.945*5:3.016 200.578*5:3.017 223.211*5:3.017 257.911*5:3.017
56.244*5:3.017 102.511*4:3.017 116.077*5:3.0
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MeganQ
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AFNI Message Board
Sorry to bother you again, but a question about shifting my timing files!
I have a regressor of no interest (called "Class") that has an onset of 0.011 in run 1 for example.
Therefore, when I apply the stim time offset of -.831, my new class_offset.1D file reads as so
-0.82:5
-0.82:5
-0.815:5
This is I believe what is causing my script to error, however I have copied t
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MeganQ
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AFNI Message Board
Hello,
I hope you are doing well!
I am trying to use AFNI proc.py to run first-level analyses on data that have been preprocessed using fmriPREP.
I specifically have a question about the regress_stim_times_offset option.
In fmriPREP, slice timing was performed on the BOLD data in the following way:
Slice time correction was performed prior to other signal resampling processes usi
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MeganQ
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AFNI Message Board
Hello!
I'm trying to use trial-by-trial behavior as a parametric/amplitude modulator and look at contrasts where I compare the modulation effects between conditions.
I saw the following post: which suggests that I should be doing the following:
-gltsym 'SYM: myCondition1[1] -myCondition2[1]'
I just want to double check that I am conceptually understanding this correct
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MeganQ
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AFNI Message Board
Thanks so much Rick!
Here's my output from cat /etc/os-release
tue50988@cla19097:~$ cat /etc/os-release
NAME="Ubuntu"
VERSION="20.04.4 LTS (Focal Fossa)"
ID=ubuntu
ID_LIKE=debian
PRETTY_NAME="Ubuntu 20.04.4 LTS"
VERSION_ID="20.04"
HOME_URL=";
SUPPORT_URL=";
BUG_REPORT_URL=";
PRIVACY_POLICY_URL=";
VERSION_CODENAME=f
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MeganQ
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AFNI Message Board
Hello AFNI gurus,
I apologize in advance for my tech knowledge deficiencies...I am trying to update our installation of AFNI on our compute resource (linux) for multiple users. I successfully updated AFNI for myself, however, when I try to do so for multiple users it seems to actually lead to making it so I can't call afni as a single user anymore either. This is what it know gives me wh
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MeganQ
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AFNI Message Board
Ah, that could do it! Here's the version:
Precompiled binary linux_ubuntu_16_64: Dec 7 2020 (Version AFNI_20.3.03 'Vespasian')
So it looks like we need to update. Unless there's an older version of the -regress_extra_ortvec option?
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MeganQ
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AFNI Message Board
Hi Rick,
I really appreciate your help on this matter! I got closer this time, but still getting some errors. I concatenated the motion and confound files into one 1D file each (with 217 (number of TRs per run)*4 (number of runs) rows) and am getting the following error:
** error: option -regress_opts_3dD follows unknown arg #107 (-regress_extra_ortvec)
Here is the terminal output when I
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MeganQ
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AFNI Message Board
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