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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 for clarifying, Rick.
So I need to decide between duration modulation (dmBLOCK) and adding temporal derivatives (SPMG2)? Is it possible to have it both ways?
I've run it both ways, although I now realize that running SPMG2 with RTs married to stimulus onset times will modulate the amplitude, not the shape, of the function.
Phil
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pdeming
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AFNI Message Board
Hi Rick,
I was originally using dmBLOCK, but switched to SPMG2 to account for the temporal derivative.
You are correct that the previous thread was using AM2. I missed that the first time. So will the code below give me duration modulated coefficients for both the regressor and its temporal derivative, if I also switch the stim time files to the stimulus onset:RT format (instead of stimulu
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pdeming
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AFNI Message Board
Hi AFNI,
Can you please clarify a few things about the -stim_times_AM1 option in 3dDeconvolve? I'd like to specify the HRF with duration modulation, but not amplitude modulation. My stim time files have stimulus onsets married to the participant's RT (stimulus onset*RT). When I run 3dDeconvolve, the log spits out the average amplitude for each regressor. With this format, am I modula
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pdeming
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AFNI Message Board
Hi Gang,
I switched over to 3dMVM, like you suggested. Now I'm getting an error I can't seem to solve. I've seen this elsewhere on the message board, but the solutions don't seem to apply.
Again, I have two within-subjects variables of interest, one continuous between-subjects variable of interest (Anx), and four covariates of non-interest (two of which are continuous).
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pdeming
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AFNI Message Board
Anxiety is a constant for each subject (between-subjects variable), so it sounds like I should go with 3dMVM.
Just to test my knowledge, am I right that the GLT below would be an even more specific test of the effect of Anxiety on Happy trials in the Standard condition?
-gltLabel 5 'Standard_Happy_Anx' -gltCode 5 'Cond : 1*Standard Emo : 1*Happy Anx : ' \
Thanks for the
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pdeming
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AFNI Message Board
Hi Gang,
I have a few questions about setting up 3dLME. I have two within-subjects variables (Condition: Standard vs. Reward; and Emotion: Happy vs. Neutral) and one continuous covariate of interest (anxiety severity). I also want to control for four covariates of non-interest: age, race (non-white vs. white), IQ and gender.
Here are my questions:
1. As I understand LMEs, I need to inclu
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pdeming
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AFNI Message Board
Got it. I knew something existed that was exactly what I wanted, but couldn't find it for some reason. Thanks for pointing me in the right direction.
Phil
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pdeming
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AFNI Message Board
Hi AFNI,
I'd like to make sure I'm modeling my stimulus events correctly in 3dDeconvolve using the BLOCK function. Is there a way to plot the onset and offset of stimuli within each condition?
Here's what I'd like to see: a plot with time on the x-axis and lines on different levels of the y-axis (one line per condition), indicating stimulus onset and the offset of the blo
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pdeming
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AFNI Message Board
Bob,
That helps me with my decision-making for now. Thanks!
Phil
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pdeming
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AFNI Message Board
Hi AFNI Community,
I'm running into a funny problem with ClustSim. As I understand, things are changing with the way AFNI runs ClustSim.
In the past, our lab has used 3dFWHMx and 3dclustSim to calculate the cluster extent threshold. I was recently told to add the -ACF option, to yield a more accurate value.
However, I also came across the new -clustsim option in 3dttest++, which see
by
pdeming
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AFNI Message Board
Hi Rick,
I found a workaround to this problem. However, for future reference, it might be good to know what my options are.
Yes, I did add the -num_glt option to the -regress_opts_3dD command. So that didn't work. When I ran afni_proc.py and tried to compute more than 10 GLTs with -regress_opts_3dD, I got an error saying I needed to use the -num_glt option to allow for more than 10 GLT
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pdeming
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AFNI Message Board
Hi AFNI community,
I'm using afni_proc.py to process an fMRI task, and I'd like to include more than 10 general linear tests. I'm using -regress_basis_multi and -regress_opts 3dD to run these tests.
The first time I ran the data through I got this error:
3dDeconvolve dies: Use -num_glt option to specify number of GLTs when more than 10
So I added the -num_glt option
by
pdeming
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AFNI Message Board