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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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Brian, Thanks for providing a link to the new documentation website. However, it is no longer working. Has the website been moved again?
Also, my questions remain unanswered. (1) Is the method that was described on that page (using 3dcalc) still considered best practice for conducting conjunction analyses? (2) Is there any consensus about the proper time (before or after) to use cluster-ext
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KendraS
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AFNI Message Board
Hi everyone,
I wanted to follow up on a discussion on the message board from a couple of years ago about cluster-extent thresholding conjunction analyses. If I'm reading it correctly, one thread recommends correcting *before* running a conjunction analysis and another thread appears to advocate for correcting *after* the conjunction analysis. Is there any consensus about the proper tim
by
KendraS
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AFNI Message Board
There should be a file upload KendraSeaman2.tar that has a conj_svcho_ep+tlrc head/brik file that are different sizes. It should also include the anatomical scan - aveanatss1mm+tlrc.
I may have uploaded the wrong directory earlier today. Sorry for the confusion on my end.
Kendra
by
KendraS
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AFNI Message Board
Hi Bob,
I just uploaded both files I'm using - aveanatss1mm+tlrc as an underlay and conj_SVcho_ep+tlrc as overlay - on the afni server as KendraSeaman.
Thanks for your help!
Kendra
by
KendraS
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AFNI Message Board
Thanks Rick. I'm not sure how that happened! I found the original header file, replaced in the folder, and re-uploaded it to the afni server. I also included the anatomical scan I have been using as an underlay, as requested by Bob.
by
KendraS
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AFNI Message Board
Thanks for the quick reply!
I don't think we have alpha on. There is no AFNI_FUNC_ALPHA set in the .afnirc file. Within the AFNI viewer the color overlay "pbar" is solid (no left-right white-color gradient).
I uploaded a copy of the file (KendraSeaman.tar) to the AFNI server as suggested in an earlier response.
Also, thanks for the reference. I'll check it out!
by
KendraS
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AFNI Message Board
Thanks for the quick response!
When I set the overlay and underlay to the same data set, it fixes the problems I was having with the viewer displaying voxels with a value of 2 while the threshold was set to a value above 2.
However, when I view the cluster report, it still includes voxels of 2 in the cluster report. I've uploaded the file to the afni server as suggested by ptaylor -
by
KendraS
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AFNI Message Board
Thanks for the quick response!
The "Overlay" and "Threshold" data sets are the same volume - there is only one brick in the file.
I just uploaded the conj_SVcho_ep+tlrc files to the server as you suggested. The file name is KendraSeaman.
Thanks again for your help.
by
KendraS
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AFNI Message Board
Hi everyone. I’m trying to do a conjunction analysis and I have some question about viewing the results.
First, I ran a conjunction analysis,
3dcalc -a zeffortSVcho_age+tlrc'[1]' -b zprobSVcho_age+tlrc'[1]' -expr 'step(a-3.28)+2*step(b-3.28)' -prefix conj_SVcho_ep
and then I opened the conjunction map in the afni viewer. This is my understanding of how to
by
KendraS
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AFNI Message Board