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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 AFNI experts,
I have a question in generating group-level maps of the functional correlation maps that is highly positively skewed.
I basically followed the steps of simple correlation analysis from seed region time series during task performance (https://afni.nimh.nih.gov/SimAna)
1) original volumes were cleaned by subtracting baseline/nuisance activity included activity from ventri
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sjmich
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AFNI Message Board
Dear Gang,
Sorry -- I replied to the wrong post.. I just attached the same post as a follow-up to your suggestion.
Thanks a lot for the suggestion. I see that centering would be a good option to remove the session effect (which is a within-ss covariate). I just have a few follow-up questions:
1) But for between-ss covariates, it is ok to residualize it (e.g., body mass on RT in case if the
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sjmich
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AFNI Message Board
Hi Gang,
Thanks for your reply. The reason to residualize all data (even the RTs) is to control potential confounds (such as session order). For instance, the two different treatment conditions (DD and PC) were given in either session 1 or 2 (was counterbalanced across subjects). Because the same task was given in two sessions, participants' RTs were generally lower in session 2 than 1 (i
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sjmich
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AFNI Message Board
Dear Gang,
I have a modelling question about 3dLME. The help page mostly describes between-subjects designs, but I was wondering about cases with within-subjects design. My main interest is on a correlation analysis between brain and behavioral data in respect to within-subjects conditions.
I have a 2 x 2 design -- both factors are within-subjects contrasts (i.e., 2 treatments and 2 cue con
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sjmich
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AFNI Message Board
Dear Gang,
Thank you very much for your reply. The covariates of no interest are between-subjects quantitative variables -- for this, then I would use 3dMVM.
But in the further analysis, I might want to pursue to add quantitative variables that are within-subjects (associated with each of w/s-condition). This would require 3dLME in the end? If it is within-subjects variable, the qVarCenter
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sjmich
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AFNI Message Board
Dear AFNI experts,
I am trying to understand the difference between 3dLME vs. 3dMVM GLT contrasts.
In brief, I have a model with all within-subjects variables of interest: 3 time (TRs), 2 scan sessions, and 2 attention conditions. I also have some nuisance factors that I am not interested (e.g., participants’ scan sequence orders, body weights, scan time onsets; all centered at 0 across sub
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sjmich
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AFNI Message Board
Thank you so much, Gang. The script runs fine now.
Best, Michelle.
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sjmich
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AFNI Message Board
Dear Gang,
I have a question regarding running 3dLME. I have two fixed factors of interest (2 categorical variables), and the rest as covariates of no interests (mean centered and quantitative). Because I wanted to see my fixed effects while all of covariates are regressed out, I used 3dLME. MSeq could be like categorical variable (as the values are 1 or -1, but I treat it as quantitative to h
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sjmich
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AFNI Message Board
Dear Gang,
Thank you very much for your input. I have been using afni version from this year January, 2016. I am trying to run with the new version. I hope the update does not affect too much of the prior analyses that I did.
Best,
Michelle
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sjmich
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AFNI Message Board
Dear AFNI experts,
I have a question how to go about FWE cluster-wise correction after a mild smoothing applied only for the group analysis.
I ran a multivoxel pattern analysis on a native space (without any spatial smoothing), but I wanted to apply a very mild smoothing just prior to the group analysis (i.e., smoothing right after spatial normalization step).
So in this case, I would like
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sjmich
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AFNI Message Board
Dear Daniel
Thank you very much for your input!
I think the viewer actually seem to pad some extra spaces when the coordinate along Left-Right is not completely symmetric (under SPM) while AFNI doesn't do so.
Best, Michelle
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sjmich
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AFNI Message Board
Dear AFNI experts,
I have a question regarding how AFNI sets the image origin (0,0,0) of the mprage (in native space) and EPI images (both in native space).
I have been using both AFNI and SPM to view MPRAGE/ANAT images, and some subjects data show no problem - same origin actually for both programs. But for certain subjects, the origin viewed using AFNI seems to be bit off from the medial
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sjmich
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AFNI Message Board
That's good to know. Then I guess the model would not be accurate anymore..
Thank you so much for your help!
Best,
SJ
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sjmich
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AFNI Message Board
Thank you, Gang.
So by that you mean that other time points (not included in TENT model) are assumed to be at 0, right?
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sjmich
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AFNI Message Board
Dear AFNI experts,
I have a quick question regarding specification of TENT function time window in GLM.
For now, I have the parameters set in a conventional way (e.g., TENT(0,20,11): to get the full response time course from 0–20s; 2s TR) after an auditory event. But as I increase the number of events (to model condition-specific events, such as animal versus speech sounds), modelling 0–20s
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sjmich
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AFNI Message Board
Thank you very much, Gang!
I tried the contrast under the glf model, but somehow the result looks very patchy (i.e., very high intensity voxels are scattered), so it seems something went wrong.
I ran the same code under glt, then it looks reasonable, but not the same as I would see on the F-map. Due to running time with many contrast, I decided to run the two sessions of the data separatel
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sjmich
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AFNI Message Board
Dear Gang,
Thank you for your response.
I just wonder though whether the Time set up as you suggested only captures every other time points are different from t0? How does it capture any difference due to t2 vs. t4, for example?
Thank you again.
SJ
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sjmich
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AFNI Message Board
Dear Gang,
I have a question regarding a set up of glf. I have 3 within-ss variables. First two variables (med and cueType) have 2 levels, and the last variable is Time (TENT) with 5 levels (t0 to t4). I would like set up CueType x Time interaction (including all 5 time points) for each med condition (separately for fixed at D and P condition), but I am bit uncertain how to specify the main ef
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sjmich
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AFNI Message Board
Thank you very much for help, Gang! The script runs fine now.
SJ
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sjmich
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AFNI Message Board
Dear Afni experts,
I set up a 3dMVM script to find effects with 2 (med) x 2 (cue) x 3 (TENT-basis), all within-ss factors (attached at the bottom). However, the script runs a bit, but throws an error (below). It would be greatly appreciated if there is any problem with the model that I have.
Thank you very much in advance!
Error:
[1] "Great, test run passed at voxel (20, 36, 30)!&
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sjmich
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AFNI Message Board
Dear Gang,
Thank you for your response. I understand that GAM and dmBLOCK does not assume the undershoot, but around 5 s, I expected the direction of effect to match the TENT model. But anyways, it seems using TENT-basis model better catches the time course.
I married the 1D files (onset:duration) term for stim_times_IM, rather than modelling different durations of delay separately. Becaus
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sjmich
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AFNI Message Board
Dear AFNI experts,
I am bit puzzled setting up my GLM as three different basis functions give different results. It would be great help to get an opinion on which of the models are plausible/appropriate for my experiment.
I have a fast-event related working memory task, in which participants remember sounds (i.e., trial onset) for a brief period of time. In the middle of the retention phase
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sjmich
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AFNI Message Board
Hi Gang and Peter,
So, the first approach to concatenate all sessions into one 3dDeconvolve is not recommended (even I concatenate motion parameters aligned relative to the start of each session). I am not sure how mean 2 datasets (Gang's approach) vs. concatenating into one GLM makes much difference, but I will investigate that.
Thanks for your help again!
SJ
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sjmich
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AFNI Message Board
Hi Peter,
Thanks for your input.
It's still unclear to me using -paired option. That is to contrast two sessions, which is not what I am interested in.
I want to see a main effect of stimulus onset activity (against 0) in overall collapsed across two sessions. Also entering covariates would be subject-wise, not session-wise in 3dttest++, which I assume covariate regressor would not
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sjmich
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AFNI Message Board
Dear AFNI experts,
I have a question on how to handle inter-session variability in performing a one-sample t-test.
To give more detail, each participant came in twice for scanning experiment, which showed a visual (e.g., face) stimulus for each trial. Basically, I would like to get a map of a main effect (no contrast is involved) of the visual stimulus onset activity from all participants,
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sjmich
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AFNI Message Board
Hi Gang,
Thank you so much for the advice!
I will definitely check out the paper soon (and yes, so each participant take one covariate value (e.g., RT)), and come back if I have further problems.
But essentially, I would set go for (1) 3-way interaction in the end (b/w-ss group x TENT x covariate) or go for (2) b/w-ss group x covariate interaction for each TENT basis? I presume to do th
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sjmich
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AFNI Message Board
Dear Afni experts,
I have read some of afni documention on the group analysis, but it was bit difficult to know which one of the analysis track (e.g., 3dLME, 3dMEMA, or 3dMVM) would be appropriate for my case:
I have a mixed design: 1 between-ss factor (2 independent-ss groups), 1 within-ss factor (time series from TENT basis function), and 1 quantitative co-variate factor (behavioral per
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sjmich
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AFNI Message Board