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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
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By item-level covariate, do you mean that the semantic distance rating was collect at each individual task level? If so, you may consider using amplitude modulation (or parametric modulation) with option -stim_times_AM2 in 3dDeconvolve. Read the details of the option in 3dDeconvolve:
3dDeconvolve -help | less
by
gang
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AFNI Message Board
Assuming you centered your covariates properly, the answer for your first question is a).
> we assume that sub-brick [2], described as "difference of slopes wrt
> covariate" shows us the areas that are correlated with the first > covariate
> (i.e. an increase in the covariate is associated with an increase in the BOLD).
Yes, that's right if you only have one
by
gang
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AFNI Message Board
andrea Wrote:
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> at the last afni bootcamp you mentioned that there
> is no function yet for 3dDeconvolve that combines
> varying stimulus duration (dmBLOCK) with the
> option of parametric modulation of the BOLD
> response (e.g., individual ratings per stimulus).
> Has this possibility been developed in the
> mea
by
gang
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AFNI Message Board
Try my second approach then:
3dttest++ using one of your conditions as a covariate
If you want to obtain specifically the correlation coefficient, you may use
1) 3dMean to get the mean for each condition;
2) 3dMean -sd to obtain standard deviation;
3) 3dcalc to standardize the data
by
gang
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AFNI Message Board
Giacomo Perri Wrote:
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> I need to do a voxel-by-voxel correlation between
> conditions A and B across a group of 40 subjects.
> In other words, I would like to find for which
> voxels activation in these two conditions covaries
> across my subject group. I just cannot figure out
> a way of doing this. Any help would b
by
gang
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AFNI Message Board
Andrew,
There are a few approaches to assessing the multicollinearity among explanatory variables in a model. One of them is the condition number of the design matrix that is used in 3dDeconvolve to alert the user about its severity. Some people do view that a correlation higher than 0.4 between two regressors indicate a potential multicollinearity issue, but that's not necessarily always
by
gang
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AFNI Message Board
> 1) which Afni program do you recommend to explicitly model
> the interaction in a repeated measures within subject design
> in a 2 x 2 Anova?
A couple of approaches:
1) 3dANOVA3 -type 4
2) The interaction can be directly obtained through a t-test with 3dttetst++ or 3dMEMA for (A1B1-A1B2)-(A2B1-A2B2).
> 2) can I re-use the individual group contrasts calculated from a G
by
gang
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AFNI Message Board
Steve Wrote:
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> I performed a contrast between two groups using
> 3dmema and included a covariate. I am actually
> interested in the regions covarying with my
> behavioral measure (the covariate), rather than
> the contrasts with covariate removed. I see that
> there are actually two covariate subbricks pairs
> (e
by
gang
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AFNI Message Board
iain Wrote:
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> To clarify, I was wondering if there was ever a
> reason to have something like this [1 -3 -1 1 3],
> an arbitrary contrast that sets some values
> positive, others negative, and they do not sum to
> zero. This is more the kind of thing that puzzled
> me. Why would someone do that? Or would they? I
>
by
gang
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AFNI Message Board
Tim Meeker Wrote:
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> I am interested in a correlation between
> functional connectivity and pain rating.
Do you mean a correlation analysis between connectivity and pain rating with BOTH brain states in one model? If so, it sounds seemingly simple, but it can't be easily done in any statistical package. I need to modify 3dLME
by
gang
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AFNI Message Board
j_richey Wrote:
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> Sorry for resurrecting an old thread, but I am
> relatively new to R, and it wasn't clear to me how
> to execute command line statements within the
> "myCmds.R" file you specify above. In bash, I
> would think that this would be something like an
> "eval" statement, but I w
by
gang
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AFNI Message Board
iain Wrote:
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> I'm wondering about the interpretation of
> non-zero summing GLTs and when and why someone
> would use them.
A contrast can be treated as a special case of general linear test. There are many cases where you may appreciate this general definition, but at least I can think of three simple scenarios where th
by
gang
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AFNI Message Board
Tim Meeker Wrote:
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> I have resting state data in different brain
> states (pain state versus non-pain state) in the
> same individuals. Each individual has different
> pain ratings during the scan. I want to regress
> the individual's pain ratings to the group t-map
> results on a voxel-wise basis, in an attempt
by
gang
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AFNI Message Board
> 1. Is it necessary to model all the stimuli (i.e., have 4 regressors in one 3dDeconvolve command)?
Yes, whatever you think have some signature in the BOLD signal should be accounted for in the model.
> 2. What is 3dDeconvolve using as the “baseline”?
The baseline condition is considered at those time points when fixation or none of the condition are present, and is modeled by d
by
gang
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AFNI Message Board
> if I want to make a 1d file that has a value of 1 at the following TRs: 10, 30, 50, 70
> and a value of -1 at the following TRs: 20, 40, 60, 80 and had 100 total TRs, how do
> I do this?
One possibility is to use timing_tool.py with something like
timing_tool.py -timing **StimulusOnsetTime** -timing_to_1D *OutputFileName* -tr *YourTR* -stim_dur *StumulusDuration* -min_frac ..
by
gang
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AFNI Message Board
John,
It looks like you can center the covariate on the overall mean and then scale by the standard deviation. If you're not sure if the two groups have the same covariate effect, it's better not to make a stronge assumption, and go with
Model:-1+Time:Group+Group:MyCov
> would it be better to set up two 3dLME analyses, one looking at each hypothesis
> (one analysis omi
by
gang
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AFNI Message Board
Most of the time there is no need to create your own regressors. With stim_times you only have to feed in the stimulus timing information. So read the help information of 3dDeconvolve (especially the part regarding -stim_times)
3dDeconvolve -help | less
Also the model should only include all the task/condition effect and confounds in the BOLD signal. All sorts of contrasts or general linear
by
gang
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AFNI Message Board
A couple of comments:
1) Covariate centering. You need to center your covariate and, better yet, scale by the standard deviation. Do your groups have roughly the same average about the covariate? If they are significantly different from each other, when you test about group difference in terms of HDR, what kind of hypothesis about the covariate value: at the overal mean of the covariate across
by
gang
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AFNI Message Board
> Would it be appropriate to average each IRF time point's beta value
> (the data has previously been converted to % change from the voxel-wise
> mean rather than absolute intensity) across the subjects in a group to come
> up with a group average IRF? Would it be better to fit a curve to each
> subject's IRF estimate and then find average values for the curve fit
by
gang
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AFNI Message Board
> am I correct to say that I should be looking at subbriks [2] & [3] of the output
> (in the case of 1-sample t-test with a covariate) where it gives me the slope
> with regard to the two variables, and a statistic associated with it?
That's all you want.
Gang
by
gang
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AFNI Message Board
> I use the default operation, -center DIFF. I did not demean the covariates. Is it correct?
Since you have one group of subjects, that should be fine.
> There is not sub-brick that is correlation coefficient between image and blood-test after remove the age effect, right?
You already have the regression coefficient for blood test, right? The correlation coefficient between z-sco
by
gang
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AFNI Message Board
HI Xiaozhen,
> According to your opinion, I did not use gender as a covariate any more.
If you prefer, you can still model the gender effect with 3dttest++ with both options -setA and -setB.
> 3dttest++ -setA subjects_image_file -covariates covariate_file -prefix test_result
Did you center your covariates? Read the help of 3dttest++ for the details regarding centering:
3dtt
by
gang
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AFNI Message Board