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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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Hello pt, thank you again for these questions and sharing your insights!
(C1) So, if you use 3dNetCorr to calculate a wholebrain correlation map, that is done by averaging the time series within each ROI and calculating each map. That is fine---is that what you want?
Yes, I think this would be in corresponding to what I did in CONN I believe.
(C2) And did you make the perform an analogou
by
Jiaxu Han
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AFNI Message Board
Hello pt,
Thank you for the follow-up questions!
(A) yes, I imported the same data into both packages for seed correlation.
(B) yes, I am using the same threshold for clustering (0.01), but as Peter mentioned earlier, the method seems different for these two softwares (random field theory for CONN, and for AFNI I used 3dClustSim).
(C) I used the program 3dNetCorr in AFNI to calculate
by
Jiaxu Han
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AFNI Message Board
Hello AFNI experts,
I conducted a seed to whole brain analysis on resting-state data using CONN and AFNI individually (also preprocessed in CONN and AFNI respectively), but these two softwares yielded different results for two seeds (i.e. no significant clusters from CONN but there were 3 significant clusters from AFNI). I am just wondering if this is even possible for different softwares to g
by
Jiaxu Han
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AFNI Message Board
Hello pt,
Thank you so much for your reply! I think I figured it out, you were right - the grids between my ROI and preprocessed image did not match, and once I fixed that the code works now!
Thank you!
Jiaxu
by
Jiaxu Han
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AFNI Message Board
Dear AFNI experts,
This is my first time using 3dNetCorr. I got an error message but I am not sure how to fix my code. Any help would be much appreciated.
1. I want to calculate seed-to-whole brain correlation matrix for resting state data. This is the code that I wrote for one subject:
3dNetCorr \
-inset $subj_dir/errts.
by
Jiaxu Han
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AFNI Message Board
Dear AFNI experts,
I am running a paired t-test using 3dttest++ function, but for some reason, it automatically generates z score sub-bricks instead of t stats. From the -help file, it seems that this would occur only if I specify "-toz" option ("* If option '-toz' is used, the 'Tstat' will be replaced with 'Zscr' in the statistical sub-brick labels
by
Jiaxu Han
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AFNI Message Board
Hello,
I am conducting a ReHo analysis on resting-state data and would like to add motion as a covariate in the group-level analysis (specifically, paired t-test using 3dttest++). My question is, what index do people usually use to control for differences in motion across groups and/or conditions? And how do I extract that from each scan using AFNI?
For example, once I finish running prepr
by
Jiaxu Han
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AFNI Message Board