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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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Dear Gang, thank you very much for your reply!
> It shows the statistical evidence/strength for the group difference for the slope effect of time.
> It would be better to show the magnitude of the group difference (the sub-brick right before the Z-values) for the slope effect of time
> (as UnderLay on the AFNI GUI).
Thanks! In fact, I am actually using the z values sub-brick to t
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AFNIuser007
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AFNI Message Board
I do have one more question regarding these results, I hope you don't mind:
Does the mathematical test in 3dLMEr, which produced the z values for my above mentioned group*time interaction effect, have a name?
Since you said chi-square results for group:time and z values for [-gltCode Int-Ctlr_over_Time 'Group : 1*Intervention -1*Control Time :'] are conceptually equivalent an
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AFNIuser007
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AFNI Message Board
Gang Wrote:
> Do you mean "-gltCode Int-Ctlr_over_Time 'Group :
> 1*Intervention -1*Control Time :' "? If so, the
> two essentially intend to achieve the same goal.
> The slight difference is due to two different ways
> to assess the statistical evidence.
Thanks for your reply. Yes, I meant the difference between the chi-sqare values (from group*time, ge
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AFNIuser007
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AFNI Message Board
Hi everyone,
I was wondering if someone could answer the following questions about reporting results for 3dlmer?
So, I have the following 3dlmer script:
3dLMEr -prefix /analysis/results \
-jobs 24 \
-resid /analysis/residuals \
-mask /analysis/grey_matter_mask.nii.gz \
-model "Time*Group+Age+Sex+(1|Subj)"
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AFNIuser007
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AFNI Message Board
Dear all,
I am trying to design a 2x3 repeated measure design for a within subject study where we have three interventions as condition and the resting state fMRI performed pre and post intervention. I want to calculate the time (pre vs post) and intervention( 3types: control,low and high) interactions.I also wanted to assess that between intervention (pre-post differences with respect to a
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AFNIuser007
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AFNI Message Board
Hi everyone,
in another thread on this forum (https://afni.nimh.nih.gov/afni/community/board/read.php?1,166126,166126#msg-166126), Gang has posted some good suggestions about result reporting (abandon strict dichotomization, report full results, quantify effects & model data hierarchy).
The original paper (https://www.biorxiv.org/content/10.1101/2021.05.09.443246v1) is focussing on bayesi
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AFNIuser007
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AFNI Message Board
> Is this clear to you?
Yep, got it now - thanks!
I'll try it out this way.
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AFNIuser007
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AFNI Message Board
Thank you very much for your answer!
>3dLMEr would not parse the specification properly even though it didn't throw an error in this case. To make sure you get the intended results, rerun the script with corrected coding.
Thanks for pointing that out!
> If you really want to address these three questions, account for the interaction between Time and outcome1 by creating a r
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AFNIuser007
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AFNI Message Board
Hi Gang, thank you for your answer!
> That seems right.
Thanks!
> In this case, it makes sense if your model contains the interaction term between Group and outcome1.
That makes sense.
Do you know why it produces a result even without the interaction effect being in the model? Would you expect the result to be different?
> So, if I interpret what you want correctly, just d
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AFNIuser007
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AFNI Message Board
Hi Gang, could I just ask a follow up question on including the outcome measures as covariates?
>> if I changed the model to Time*Group+Age+Gender+outcome1+outcome2+outcome3+(Time|Subj) , in order to be able to look at the effects of those outcome scores, I am basically correcting for them, am I not?
> With this specification, you would be able to assess the association of each outco
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AFNIuser007
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AFNI Message Board
Hi pt, thanks for the update and your feedback!
Greatly appreciated!
- 007
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AFNIuser007
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AFNI Message Board
Just cross-referencing some information here about 3dMSS from another thread (where @Gang was helping me out with 3dLMEr), in case someone is using 3dMSS and has the same questions:
"My model is for a longitudinal study with two groups and measurements (...)"
>Your current model assumes a linear relationship of Time. In case nonlinearity is of interest, consider 3dMSS.
&
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AFNIuser007
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AFNI Message Board
Thanks for your reply, very helpful!
> -mrr 's(Time,k=7)+s(Time,by=Group,k=7)+Age+Gender'
According to the 3dMSS, I would create a pred.txt that include label, Time and Group (binarized).
Are Age and Gender okay to only be in the dataTable (not the pred.txt), and would Gender have to binarized for 3dMSS?
> With this specification, you would be able to assess the associat
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AFNIuser007
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AFNI Message Board
Thank you very much for your reply and the warm welcome, Gang!
>With a longitudinal study, you may try to account for varying slope effect:
>-model "Time*Group+Age+Gender+(Time|Subj)" \
That is a good idea, thank you! Btw, in lme4 (Time|Subj) is the same as (1+Time|Subj), if I am not mistaken? (Random intercept and random slope)
> By default, 3dLMEr centers a quantit
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AFNIuser007
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AFNI Message Board
G'day everyone,
I was wondering if someone could check if the contrasts that I've written for 3dLMEr are correct?
Our study is different than the examples put foreward in the help file, therefore I'm not 100% certain and would really appreciate some confirmation :)
The following model is for a longitudinal study with two groups and measurements after 0,2,4,... months.
We un
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AFNIuser007
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AFNI Message Board
Hi --pt,
first of all, thanks for your answer!
I was able to replicate your exampe for the AFNI_data6 func slim file, but it still is different for my dataset.
Regarding the difference between bisided and 2sided: Your're right, I should use bisided, as there's a chance that positive and negative voxels might happen to be next to each other. But there's no -bisided option in
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AFNIuser007
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AFNI Message Board
Hi everyone,
I've just been comparing commands with 3dClusterize and 3dclust and I'm wondering why the mean, SEM and max intensity differ?
3dclust -nosum -no_1Dformat -1dindex 5 -1tindex 6 -2thresh -2.8 2.8 -NN2 33 file+tlrc
Volume CM RL CM AP CM IS minRL maxRL minAP maxAP minIS maxIS Mean SEM Max Int MI RL MI AP MI IS
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AFNIuser007
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AFNI Message Board