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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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Grant opportunity: Third Annual a2 Pilot Awards Request for Applications on AI and Aging
Deadline: July 31, 2023 (5 p.m. ET)
Launched by the NIH’s National Institute on Aging (NIA), the Artificial Intelligence and Technology Collaboratories (AITC) for Aging Research program—or a2 Collective—is dedicated to helping Americans live longer, healthier lives through the application of AI and emergi
by
gang
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AFNI Message Board
Thanks for sharing the experience! A tool will be available soon that could check this type of issues.
by
gang
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AFNI Message Board
Luke,
The suggestion of adding another region as a covariate in bivariate correlation analysis can be as controversial/problematic as "global signal regression". Technically you can add a covariate using the option -stim_file or -stim_base in 3dDeconvolve.
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gang
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AFNI Message Board
What do you get if you run the following command in R?
install.packages('car')
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gang
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AFNI Message Board
> the random noise showing in the ventricles, cerebellum and outside the brain is fine in this case?
The model at the population level in this case (two-sample t-test) is pretty simple and straightforward. By "random noise", they could include issues such as data quality (e.g., alignment), processing, head motion, physiological confounds, etc.
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gang
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AFNI Message Board
RJ,
>> the results of a paired t-test
I assume that you're comparing two groups. So, it would be a conventional two-sample (not paired) t-test.
>> The results look off in the sense that connectivity shows in regions like the ventricles, cerebellum, and even outside the brain. Is this correct?
The results in some of those regions you mentioned are likely random noise,
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gang
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AFNI Message Board
Will,
Is it possible that you have some extra space(s) after the backslash of the following line?
3dICC -prefix /home/wgraves/data/whitehall/r01/data/hera_mnt/single_word/fmri/2001_S40/func/2001_S40.ICC3 -jobs 14 \
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gang
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AFNI Message Board
> symptoms at a follow-up time point are being explained by an interaction between a 'risk' variable (between-subject) and functional connectivity
> -model 'RISK*BRAIN_FC+COV1+COV2+COV3+(1|COV4)' \
Let's backtrack a little bit. So, 'RISK' is a between-subject factor? There is no within-subject variable? And what is this part '(1|COV4)' for?
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gang
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AFNI Message Board
In the most recent scripts you showed, it does not appear that you did the following:
Change
-qVars "COV1,COV3" \
to
-qVars "COV1,COV3,BRAIN_FC" \
Also, this line
-gltCode brainXrisk_high-low 'BRAIN_FC : RISK : 1*high -1*low' \
should be
-gltCode brainXrisk_high-low 'RISK : 1*high -1*low BRAIN_FC :' \
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gang
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AFNI Message Board
Change
-qVars "COV1,COV3" \
to
-qVars "COV1,COV3,BRAIN_FC" \
Also check out this:
" -vVars variable_list: Identify voxel-wise covariates with this option.
Currently one voxel-wise covariate is allowed only. By default
mean centering is performed voxel-wise across all subjects.
Alternatively centering can be specified through a
by
gang
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AFNI Message Board
A couple of suggestions:
1) You need to explicitly specify the model using the option -model
2) Add "-vVars BRAIN_FC" to your 3dLMEr script
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gang
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AFNI Message Board
> If I remove one of the three contrasts it would show me a similar omnibus test?
Yes, it should.
> I could use gltCode to compare two groups as well like a post-hoc test, right?
That's right. You can also specify the omnibus test for the three groups using gltCode since it's a test with one degree of freedom:
-gltLabel 1 'omnibusF' -gltCode 1 'group :
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gang
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AFNI Message Board
3dMVM automatically provides an omnibus F-statistic for the comparisons among the three groups. In addition, your -glfCode specification is rank deficient - only two of the three are needed.
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gang
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AFNI Message Board
Hans,
The option -corStr in 3dLME was added solely for the purpose of capturing the temporal correlation (i.e., AR1) when hemodynamic response curve is the input. So, any other structures for residuals are not supported at the moment.
My experience seems to show that, under most circumstances, fine-tuning fixed- and random-effects are more crucial than the residuals. For example, I might t
by
gang
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AFNI Message Board
> COV (mean framewise displacement) is (I believe) a within-subject variable.
So, COV varies across the combinations among the three factors W1-3 for each subject?
> Is it possible to specify corSymm instead of corAR1?
corSymm() is used to specify the variance-covariance structure in the residuals. I would not worry too much about the residuals. Instead, it might make sense to try
by
gang
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AFNI Message Board
> why the F-test and t-test came different?
You can verify this by checking whether the squared t-value is about the same as the F-square.
> there are 11 clusters for F-test and 10 for the t-test
Find out why that extra cluster failed to survive the t-test. Possible reasons: 1) approximation, 2) one-sided vs two-sided. Change your cluster or p-value threshold, and see what happens.
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gang
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AFNI Message Board
> 3 within subject repeated measures (W1-3) and 1 covariate (COV)
Is the covariate COV a within-subject or between-subject variable? How many levels does each of the three factors W1-W3 have?
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gang
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AFNI Message Board
Thanks for the feedback!
If the output value at a voxel is NaN (not a number), 3dLME changes it to 0 when writing out. It is not clear why NaNs occurred in your case. To pinpoint the issue, I may have to request for data sharing.
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gang
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AFNI Message Board
Vasco,
I assume that 1) you're writing your code; and 2) you're quantitatively coding the three groups with -1, 0, and 1.
To properly handle three groups, you need two variables (plus an intercept). The following example demonstrates the coding strategy (with group3 as the base/reference level):
G1 G2
group1 1 0
group2
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gang
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AFNI Message Board
In addition to what Rick pointed out, change the column name "Group" in the table to "group".
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gang
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AFNI Message Board
Nick,
> I'm trying to run a correlation analysis between brain functional connectivity and scores on a questionaire
Is this a whole-brain population-level analysis? Is your model like the following?
FC ~ scores
If so, you may use 3dttest++.
by
gang
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AFNI Message Board
> how I might calculate and show an effect size for the group level analysis?
If you perform your population-level analysis with Fisher-transformed correlation values, you can covert them back to correlation values:
3dcalc -a Grp_Result+tlrc'[0]' -expr 'atan(a)' -prefix GrpR
3dcalc -a Grp_Result+tlrc'[0]' -expr '(exp(2*a)-1)/(exp(2*a)+1)' -prefix
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gang
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AFNI Message Board
The error message is not about 3dMVM per se, but likely due to permissions or space exhaustion: .
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gang
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AFNI Message Board
Silvia,
> How can I implement FWHM in my analysis? More specifically, in the second-level analysis, I should use the acf obtained
> from the mean group (3dttest++) or that one at individual level (from 3dDeconvolve)?
There is no definite answer for this. It seems that people have been empirically estimating ACFs using the individual-level or population-level data.
> Is it corre
by
gang
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AFNI Message Board
> It's 3dMVM and afni version 21.3.06 'Trajan'.
It's likely due to an old version of 3dMVM. Update your AFNI:
@update.afni.binaries -d
Those 2 lines of GLFs can be added to your GLTs since they are essentially comparisons with one degree of freedom.
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gang
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AFNI Message Board
> Is it a correct practice to use a p-value of 0.05 for a voxel-wise analysis run in a small ROI?
It is preferable to adopt a modeling approach that is less sensitive to the amount of the data. You may consider the highlight-but-not-hide reporting methodology:
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gang
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AFNI Message Board
Are you talking about 3dMVM or 3dLME/3dLMEr? What is your AFNI version?
afni -ver
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gang
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AFNI Message Board
JW,
A recent fix should take care of this. So, update your AFNI:
@update.afni.binaries -d
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gang
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AFNI Message Board
Yuhan,
Update your AFNI:
@update.afni.binaries -d
Let us know if the problem persists.
by
gang
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AFNI Message Board
Dante, 3dLME treats those strings under the column "InputFile" as filenames. No mechanism is implemented as command lines.
by
gang
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AFNI Message Board
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