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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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It sounds like you do want to use 3dClustSim, but you first need to run 3dFWHMx on your first-level residual data. And use the acf options, not fwhm. See Andy's intro, for example:
On the other hand, if you're just exploring your pilot data results, I recommend just opening your uncorrected stat maps in a viewer and thresholding manually.
Best,
Andrew
by
Andrew Davis
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AFNI Message Board
The 3dClustSim docs also say, under the -fwhm option, "This option is no longer recommended, ...". I think that unless you're trying to do something special that falls outside the usual multiple-comparison workflow, and you know what you're doing, you shouldn't use that option.
QuoteLuisaBoh
But the last part reffers to the combination with the 3dFWHMx
What are you
by
Andrew Davis
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AFNI Message Board
I'm running a model through 3dLMEr that includes 33 gltCodes and 6 glfCodes. This is a repeated measures design with 3 study groups and 3 measurement time points from each subject. The random effect structure has subject nested within site. I'm copying in the script that runs 3dLMEr below in case it's helpful.
The output seems reasonable, except that a few of the sub-bricks whic
by
Andrew Davis
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AFNI Message Board
Haha, yes, that's fair enough, thanks Gang. In the meantime I have used my lower-level residual files for 3dFWHMx, so I think I'm all set.
Best,
Andrew
by
Andrew Davis
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AFNI Message Board
Sorry, my wording was unclear -- what I meant was that the '-resid' option from 3dLME is not available in 3dLMEr. I noticed that the documentation for '-resid' is present in 3dLMEr's code, but is commented out -- I guess I was hoping you might say, "Oh yes! I've already re-implemented -resid in my copy of 3dLMEr, let me just push it up to github."
Best,
by
Andrew Davis
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AFNI Message Board
Hi Gang,
It seems like the -resid option from 3dLME has been removed, or is not yet implemented, in 3dLMEr. Is there a way to get residuals from 3dLMEr? I'm asking because I would like to do multiple comparison correction on the output, by feeding residuals into 3dFWHMx -acf. Is there another way?
Thanks,
Andrew
by
Andrew Davis
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AFNI Message Board
This new program looks great. Just going through the documentation, a couple of notes:
- The `-formula` lines in the examples appear to be missing closing quotes
- In the documentation for the new @table syntax in the `-dataTable` section, item 4), there is the sentence:
Backslash is also not needed at the end of each line, but it would cause any problem if it is present.
Are we
by
Andrew Davis
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AFNI Message Board
Thanks very much, that will be more convenient. In the mean time, I've been using the following check:
3dTrackID -mode DET ... <more arguments> \
|| { es=$?; [[ $es == 1 ]] && true || echo "3dTrackID exited with error code ${es}..."; }
This allows the script to keep rolling if it gets exit status 1, but it will be nice to remove that and have the script hal
by
Andrew Davis
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AFNI Message Board
I have a question about the exit status of 3dTrackID after an apparently successful run. 3dTrackID seemed to complete its tasks just fine, and I got my expected output, but it exited with exit status 1 rather than 0. Can anyone tell me why? When it exits with code 1, it interrupts my bash script, since I include the option 'set -o errexit'.
Here is my command and the output:
u
by
Andrew Davis
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AFNI Message Board