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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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Dr. Taylor,
Thank you very much! This is very helpful and exactly what I needed!
Cheers,
~Nate
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Nathaniel Harnett
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AFNI Message Board
Hello AFNI Wizards!
Apologies if this question has been asked (I did try a quick search):
I am attempting to perform some basic probabilistic tractography with 3dTrackID. I know for 3dDWItoDT, the gradient vectors file should omit the G0 line. For 3dDWUncert, should the gradient vectors file (-grad option) *also* omit the G0 line, or should that be included for this program?
Thank you i
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Nathaniel Harnett
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AFNI Message Board
Awesome! Thanks for passing along! Looking forward to the new changes!
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Nathaniel Harnett
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AFNI Message Board
Brilliant! That works great!
Thanks again!
~Nate
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Nathaniel Harnett
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AFNI Message Board
Awesome! Thanks Dr. Chen!
Out of curiosity, now that I have a dataset of p-values, is there anyway within AFNI to calculate the q-values (i.e., an option in 3dFDR, given the dataset is not technically a non-statistical dataset)?
Thank you once again!
~Nate
by
Nathaniel Harnett
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AFNI Message Board
Greetings everyone,
I have a quick question on generating p-values from datasets in AFNI.
I have a 3 3dDatasets. One dataset contains coefficients (X), one contains the mean (Mu), the other contains standard deviation (SD). I would like to get the corresponding p-value (2-tailed) for these values. I've modeled my 3dcalc code after SAS commands, where the pvalues would correspond to one
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Nathaniel Harnett
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AFNI Message Board
Hi Gang,
Yes, I am trying to look at non-linear effects in the data.
"One possible (and simple) model is
-model 'Cond*loc+Cond*age+Cond*weight' "
Oh, good! I had that thought yesterday before I saw your post. That model ran beautifully and gave data consistent with what I expected.
Thank you very much!
~Nate
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Nathaniel Harnett
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AFNI Message Board
Hi Gang!
Thanks for the input! "Loc" is a single value for each person and doesn't vary between conditions. I thought about using MVM but forces beyond my control are really pushing for LME. I'll try specifying the model in a different way and hopefully that'll fix it.
I do have another question though:
Say I wanted to look at the effects of other between-subjec
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Nathaniel Harnett
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AFNI Message Board
Greetings everyone!
I'm having a little bit of trouble with 3dLME. Specifically, I'm trying to set-up several glt's to test effects of my covariates. That is, how does the response in condition A (or B or a linear combination) vary across the levels of my continuous variable (loc). I've tried to follow the example listed on the AFNI program page, but I cannot get it to work
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Nathaniel Harnett
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AFNI Message Board
Hi Gang,
Ah! I see now! Though, I would like to double-check something else if you wouldn't mind. I have initially reset my specification matrix as:
A1 A2 A3
A1 0 0 NA
A2 0 0 NA
A3 NA 0 0
However, this only works by selecting the "direct" option, giving me an Instaneous effects matrix that ends with "NULL" and t-values that are ridiculously strong.
Usin
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Nathaniel Harnett
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AFNI Message Board
Hello again,
I have graduated from asking mundane questions about PPI to asking mundane questions about 1DSVAR.
I am having an issue choosing between either the Iterative or Direct, similar to another problem from last year:
Error Message:
Numerical scheme (0: Iterative; 1: Direct)? 1
Error in SVAR(x = fm, estmethod = "direct", Amat = instMat, Bmat = bb, :
Model is not i
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Nathaniel Harnett
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AFNI Message Board
Yes, we do not see statistically significant results at the seed region in the group output for either a) the interaction coefficient, or b) the seed time series coefficient. Does that make sense?
Aside from our confusion over not seeing group level statistical significance for b (e.g., seed time series before psychological interaction) in our seed region, I am *very* happy with the whole anal
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Nathaniel Harnett
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AFNI Message Board
Hello, oh AFNI Masters,
I recently got the PPI code on Gang's homepage to run without erroring out, and to produce timecourses that (look) alright. We're using Broadman Area 25 (bilaterally) for our mask, warping the tlrc version back to orig space, and then using 3dmaskave to get the time course. From there, we're just borrowing Gang's code.
However, we noticed in our
by
Nathaniel Harnett
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AFNI Message Board
Thank you for the prompt response!
Just to make sure I understand, by not setting the voxel size to our native resolution, I'm essentially asking AFNI to apply warping to a much finer resolution than we originally had? This would probably explain the exponential growth in file size then.
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Nathaniel Harnett
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AFNI Message Board
Hello!
I am attempting to run a simple correlation analysis on a subject, and have been following Gang's guide. Things seem to be going well, however I had a question on the adwarp step. I'm warping our -data parent to the subject's anat+tlrc, however when I do this, the file that comes out is approximately 5GB in size, which doesn't seem right.
The script is set up as:
by
Nathaniel Harnett
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AFNI Message Board