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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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Awesome, that is very much in line with what we are seeing!
Best,
Lea
by
lmm194
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AFNI Message Board
Hi Rick,
Using a mask does change things and actually we realized yesterday that we were looking at data what had not been blurred (we will be running MVPA down the road), so I *think* that also explains the reduction in the thresholding values - because you take a hit when you blur, right?
Thanks!
Lea
by
lmm194
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AFNI Message Board
Hello,
Our lab is seeing an unexpected result when we rerun our data using -acf for clustsim (compared to the -fwhm method). Our cluster sizes are smaller, much smaller, going from 17.2 voxels at .001 with fwhm, to 3.7 voxels at .001 with acf. This is when looking at the full grid - we now go with a whole brain mask, but in the interest of comparing the fwhm and acf we did the exact same clus
by
lmm194
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AFNI Message Board
Hello,
I was wondering what the " XXXX vectors are constant" warning in 3dttest++ indicates? I've seen if before, but cannot find documentation on what exactly it means or if it is a serious issue over a certain number.
Thank you!
Lea
by
lmm194
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AFNI Message Board
Of course ten minutes after I posted this I figured out that I needed to resample the cluster maps so they were in the same resolution as my functional data....
by
lmm194
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AFNI Message Board
Hello,
I am trying to run 3dROIstats for an ROI analysis, but both the masks I am giving it appear to have far more voxels than my data (583968 compared to 172800). The masks originally were from ALE analyses, but at this point are converted to cluster mask format . When I look at their 3dinfo, they are much larger files than other masks I have successfully used. In afni the only non-zero v
by
lmm194
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AFNI Message Board
Hello,
I'm am seeing some of the same errors and was wondering if anything else been figured out with regard to this?
Errors -
** Error:
Expecting more than 4 parameters for option "-set".
Have 1 parameter(s) in string "pos" instead.
**Error:
Error parsing arguments. See 3dMEMA -help for details
021: Command not found.
-model_outliers: Command not found.
by
lmm194
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AFNI Message Board
Hi Rick,
Thank you so much for getting back to me about this!
Lea
by
lmm194
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AFNI Message Board
Hello,
I'm using make stim time to generate our timing files and some of our conditions only occur in later runs. In the past when I've done this I have seen a single asterisk in the empty run, but this time if the first run is empty for that condition, I get a double asterisk. Why is only the first run marked with a double asterisk and is this an issue (see below for example)?
by
lmm194
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AFNI Message Board
That was the issue... I had left off the -paired option, ugh such a little thing can cause so much grief! Thank you so much!
by
lmm194
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AFNI Message Board
Hello,
I am interested in comparing two different stimuli classes wordsVhouses and found that when I look at the output for when I have 3dDeconvolve do the comparison and the output for when I do a two sided t-test in ttest++ they are different.
In the first case I compared wordsVhouses as a GLT in my 3dDecon script and then put that subbrick into 3dttest++ as a one sided t-test. In
by
lmm194
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AFNI Message Board
Rick,
Thank you very much for taking the time to explain that to me. It is very helpful.
Best,
Lea
by
lmm194
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AFNI Message Board
Thank you both for your help. This is an experiment that I did not design that was "orphaned" and I am picking it up to analyze. It is based on a previously published study.
The design is as follows:
There are 3 stimulus classes: 1) faces, 2) houses, 3) font
There are 2 runs of 420 s (210 2s TRs)
In each run there are 7 blocks of each stimulus type lasting 20 s each
Withi
by
lmm194
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AFNI Message Board
Hello,
I have been having an issue with the block specification in 3dDeconvolve and was hoping for some advice. I have 20 sec blocks (ten 2-sec TRs) of stimulus one after the other (no breaks). When I first ran the afni_proc.py script I specified my BLOCK with d as 20 (thinking it was in seconds) but this lead to extreme overlap of my blocks (to the point that AFNI was giving multiple corre
by
lmm194
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AFNI Message Board