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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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Hi Gang,
Sorry for my delayed reply. I just saw your response!
I wanted to report the F stat- the intercept is meaningful in my case.
Thank you
by
kathrynj
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AFNI Message Board
Hi Sophia and Rick,
My colleague and I also noticed that for some subbricks in our respective studies, the max F value listed when using 3dclust was 100. Does the program max out at 100? Is there some sort of conversion we should use to get the exact F value (if it is indeed higher than 100)?
As a side note, we both ran first level models in SPM but then switched to AFNI later on down the roa
by
kathrynj
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AFNI Message Board
Hi Rick,
Thank you very much for your prompt reply.
To clarify, in the past, prior to changing my library path, when I selected bi-sided, I could change it to say "yes", then apply and set that value. If I were to immediately open up clusterize button again, before selecting a new contrast, it would show my currently selected values: NN=3, k=30, bi-sided=yes.
Now, when I do this,
by
kathrynj
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AFNI Message Board
Hi Peter,
I am sorry to bother you again. I noticed that while I can now change the p value, when I select bi-sided? "yes" and select "apply" and "set" it keeps bi-sided set to "no". I have closed and reopened AFNI but this error persists.
I ran the afni system check, with the output provided below:
psy-bdl-macpro-dsn:3dMVM_noresiduals kathrynj$ afni
by
kathrynj
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AFNI Message Board
Hi Gang
Thank you so much for your help! I ran 3dMVM and I think the residuals modification worked well! Can I ask a few follow-up questions, just to make sure I did things correctly since I am trained in SPM?
I ran 3dMVM with the residual flag.
3dMVM -prefix SCEfull -jobs 7 \
-bsVars "group" \
-wsVars "emotion*perspective" \
-SS_type 3 \
-mas
by
kathrynj
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AFNI Message Board
Thanks so much for your feedback. I apologize for my delayed reply; I was out of town.
To confirm, would that mean I could either use the "write cluster" or "save mask" option (either use the "write cluster" option for each cluster for each rx-level contrast or just selecting the "save mask" option once for each rx-level contrast) to make a mask of the c
by
kathrynj
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AFNI Message Board
Thank you, James and Daniel. I had been using the slider, since manually changing the p-value was not working for me. I was hoping to manually type in the p-values for enhanced precision. Peter's fix worked- my issues were related to X-11.
Thank you for this code, Daniel!
by
kathrynj
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AFNI Message Board
It worked! Thank you! I have shared this with our lab, since several people were having this issue. Have a great day!
by
kathrynj
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AFNI Message Board
Hello,
Our lab wants to extract parameter estimates from group-level clusters to tease apart simple effects. (We are used to doing this in SPM using marsbar.) We are currently under the impression that we want to do this by saving a mask of the group-level contrast like a 2x2 interaction (using the "save mask" option on the cluster table; so it includes all clusters per group-level con
by
kathrynj
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AFNI Message Board
Hello,
I am unable to enter values using the afni gui when viewing my results. Buttons/sliders work (i.e., I can change the NN level under "clusterize" using the up and down arrows; I can change the p-values using the slider tool) but I cannot type in values (i.e., I cannot type in the NN level or voxel number under "clusterize" or the p-value); I see a cursor in the entry bo
by
kathrynj
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AFNI Message Board
Hi Gang,
Thanks so much for your reply!
I am currently working on my dissertation analyses (set to defend this summer), so if it is possible to implement this feature in time, that would be fantastic.
by
kathrynj
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AFNI Message Board
Hello,
I am running a repeated measures ANOVA in 3dMVM, and I would like to used the residuals of my group level model for thresholding purposes (calculating smoothness estimates by averaging subject level spatial autocorrelation function (acf) parameters based on individual subjects’ residuals from the group level models). Is this possible?
Thank you very much,
Katie
by
kathrynj
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AFNI Message Board