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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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Hi Gang,
Thank you for your reply. Yes, that is correct, comparing two groups - thank you for clarifying.
So just to confirm, the random noise showing in the ventricles, cerebellum and outside the brain is fine in this case?
Thank you!
RJ
by
RJ
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AFNI Message Board
Hello,
I was wondering if someone can please assist with viewing the results of a 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?
Please see the screenshots of the results attached (includes paired t-test and paired t-test with clustsim).
Please see the script I am running be
by
RJ
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AFNI Message Board
Hi Rick and Paul,
Thank you both for trying and replicating the command!
So adding the complete name (NAME.nii, NAME.nii.gz, NAME+orig, NAME+orig.HEAD) was still giving the error, and running the brew install netpbm didn't install the package for some reason, same thing with updating the binaries.
The command:
# /bin/bash -c "$(curl -fsSL ;
returns: undefined variable error
by
RJ
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AFNI Message Board
Hello,
We are running into an issue when running the 3dTqual option, the error is as follows:
# Can't read from -stdin
Our script is:
# 3dTqual -range -automask rest_fmri_file | 1dplot -one -stdin -png /qualitycontrol/motion/fMRI_tqual
Running the above line was previously producing the plot.png, but an output is no longer being produced and the above error appears.
Any sugges
by
RJ
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AFNI Message Board
Noted, thank you! We'll look into the bandpassing with our acquired short TRs. Appreciate the suggestions and assistance!
by
RJ
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AFNI Message Board
Hi Rick,
Thanks so much for your reply and suggestions!
0. TR is .72 with 667 volumes
1. Initially we were completing it twice, but are no longer trimming the masks
2. It does look like valid time series
3. We think the regressors did not project out based on the results of the one-sample and paired-samples t-test, we are still finding signal in the ventricles, WM, cerebellum etc.,
4.
by
RJ
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AFNI Message Board
Hello,
I am trying to extract time series and am using the command below:
3dmaskave -q -mask /Volumes/masks/SN_resam.nii.gz \
func_task_pp_ICAaroma_bptf.nii.gz \
> /Volumes/subjects/${subj}/${subj}_SN.1D
However, am getting the error:
Input dataset func_task_pp_ICAaroma_bptf.nii.gz grid mismatch from mask.
*** Input and mask datasets are not same dimensions!
I've tried the
by
RJ
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AFNI Message Board
How can I invoke the -ClustSim option in 3dttest++?
For example my script is the following:
3dttest++ -ClustSim -AminusB -prefix /Volumes/groupanalyses/SN_ASDvsSSD.nii.gz \
-setA \
-setB \
But I am getting the following error:
++ 3dttest++: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 8
++ option -setA :: processin
by
RJ
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AFNI Message Board