Show all posts by user
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
Page 1 of 3
Pages: 123
Results 1 - 30 of 74
ah, that's smart. I just wanted to add that I noticed that if I am looking at the data in video mode it is a lot slower if all three view windows are open. While I get that of course drawing to three windows takes more processing than drawing to one window, I'm still surprised that there would be any effect...I'm on a quad core imac with 16 GB RAM.
Do you find that you have
by
jkeidel
-
AFNI Message Board
hi Rick
I tried to respond to this before but maybe I wasn't logged in? In any case, I moved the .afni.startup_script out of my home directory and that solved everything...thanks for the help!
JK
by
jkeidel
-
AFNI Message Board
hi all
Ever since I upgraded OS X to 10.12 AFNI has started much more slowly than it used to (I have also upgraded AFNI to the most recent version). All the windows flicker a lot and change positions and so it takes about 5 seconds before it can be used. Of course this isn't a super long time and I could deal with it but this also affects some other functions. For instance, watching a
by
jkeidel
-
AFNI Message Board
It is now my life's goal to find something that AFNI cannot do (within the bounds of MRI of course).
by
jkeidel
-
AFNI Message Board
hi Bob
I've been using AFNI for almost 15 years and it still does not cease to amaze me. Thanks.
James
by
jkeidel
-
AFNI Message Board
Thanks Bob. To be honest, I intended to add to that post that there was probably a way to do it in AFNI that I was just unaware of, but then I forgot to write that. It certainly didn't come as a surprise that AFNI was one step ahead of me.
In any case, since we're on a roll here, there is one other thing I was wondering about. It would be great to have a way to automatically mask
by
jkeidel
-
AFNI Message Board
hi AFNI lords
I was thinking, I often have a directory with output files from a bunch of participants in standard space, but no anatomical underlay. So I made an alias that will link in a template. But ideally, there would be some way in the AFNI controller to specify that instead of a file in the current directory, I would like one of the templates in the main AFNI directory as my underlay.
by
jkeidel
-
AFNI Message Board
Hi all
It appears to me that adding -BminusA to a 3dttest++ command using -singletonA has no effect on the output volume, even though the text output of the program says "results are SetB - sngltnA". Can you reproduce this? my commands were:
3dttest++ -singletonA stats.p1+tlrc'[3]' -setB "stats.s*HEAD[3]" -prefix PvsC
3dttest++ -singletonA stats.p1+tlrc
by
jkeidel
-
AFNI Message Board
hi Kathryn
Just to give you a quick answer to your side question--yes, if you right click on the displayed p value below the slider a menu comes up, one of whose options is to set the p-value.
James
by
jkeidel
-
AFNI Message Board
hi
you can add '&' to the end of your command to run it in the background, allowing you to continue working in the terminal while the despiking is done:
3dDespike run1+orig >>& despike.out &
hope this helps.
James
by
jkeidel
-
AFNI Message Board
thanks a lot Gang, that makes sense. it's interesting though--we had no expectation of an anticipation effect (and it's not that big), but it does seem to be there. good to have both options I guess.
James
by
jkeidel
-
AFNI Message Board
hi Gang
thanks a lot for your response. I have a few questions.
1) I'm still confused about whether it is justified to ignore any pre-stimulus anticipatory effects, which is what TENTzero seems to do. And yet, at least in my case the stats come out the same, it's really just a question of how the plotted responses look.
2) Could you explain to me, more generally, why TENTze
by
jkeidel
-
AFNI Message Board
hi Gang and Bob
QuoteGang -- didn't you get TENTzero and TENT exactly reversed in the previous post!?
I think this is really what I'm trying to figure out. I can imagine why there might be anticipation-related differences between the two conditions--one condition is blocks of the first halves of videos and the other condition is blocks of corresponding second halves. So in a sens
by
jkeidel
-
AFNI Message Board
hi all
Could someone give me some advice on plotting curves that are generated by analyses using TENT vs TENTzero? I have an analysis in which I use either TENT or TENTzero to model some responses to videos, then use 3dANOVA3 to test the group differences. While the statistical maps are more or less the same, the plotted graphs tell different stories. Specifically, when using TENT the graph
by
jkeidel
-
AFNI Message Board
I've got my guesses...who knows what other hidden joys are to be found in the source code?
JK
by
jkeidel
-
AFNI Message Board
hi all (esp. Bob)
Yesterday I noticed that every time I started AFNI the same photo appeared on the splash screen. A look through the source code revealed what was going on. It was a nice distraction from working. I don't know if this has been mentioned on the list before, but I won't spoil the "fun" for anyone else. Though maybe Ramon y Cajal could be added? Broca mayb
by
jkeidel
-
AFNI Message Board
hi Dennis and Gang
Is this a case where instead of having PE and LR as separate regressors, the values of PE and LR for each event should be specified using stim_times_AM2?
From the help:
-stim_times_AM1 and -stim_times_AM2 now take files with more
than 1 amplitude attached to each time; for example,
33.7*9,-2,3
by
jkeidel
-
AFNI Message Board
hi Gang
within-subjects, one factor with three levels, so 3dANOVA2 -alevels 3 -blevels 21 -type 3
JK
by
jkeidel
-
AFNI Message Board
hi Gang
while we are on this topic, is there currently a robust way to handle FWE correction on the results of a one-way ANOVA? That is, I cannot reformulate the contrast to be handled by 3dttest++.
thanks
James
by
jkeidel
-
AFNI Message Board
actually, I am a bit confused. I did a full deletion/reinstall of AFNI and the help says that -clustsim has not been tested with one-sample/paired tests but the afni history says
Quote08 Jul 2016, RW Cox, 3dttest++, level 3 (MAJOR), type 6 (ENHANCE)
Extend -clustsim option
Covariates and centering
1- and 2-sided
unpooled and paired
1 sample as well as 2 sample
so
by
jkeidel
-
AFNI Message Board
hi all
just wanted to reask the question from Peter above, specifically whether:
QuoteThe code runs fine without -clustsim, which suggest that this option is still not available for one sample tests. Is that true?
I just updated my AFNI and the 3dttest++ help still says that the option is untested for one-sample/paired t-tests. So is the current AFNI advice to not use -clustsim for thes
by
jkeidel
-
AFNI Message Board
hi everyone
I am posting to this thread because I have basically the same questions. I know Bob has answered similar questions elsewhere but I cannot find answers to these particular ones.
QuoteWhy are there MORE voxels required to meed 1-sided thresholding here?
I think this has to do with the difference between the terms 'one-sided' and 'one-tailed' as it applies to
by
jkeidel
-
AFNI Message Board
hi Gang
Thanks so much. I think I've got it now, and I really appreciate the help.
One "quick" thing:
QuoteAveraging does change the cross-subject variability especially when the precision/reliability information due to the averaging step is typically not taken into consideration.
Is there a way to quantify the change in cross-subject variability? Via simulation or som
by
jkeidel
-
AFNI Message Board
hi Gang
thanks so much for your advice. I just want to clear up a couple of points:
Quote1) To avoid any double-dipping accusation, it would be better to just run voxel-wise analysis on the whole brain instead of focusing on individual ROIs. With a one-way repeated-measures (or within-subject) ANOVA with three levels, you can simply run three separate paired t-tests, which can also be obta
by
jkeidel
-
AFNI Message Board
hi all
We have a study with three types of video clip: no context (NC), low context (LC) and high context (HC). We have rerun an analysis based on criticisms from a (very savvy) reviewer and I want to see whether we are making any errors that would cause our conclusions to be invalid (for the purposes of the study I am happy if the tests are overly conservative but not if we are in any way do
by
jkeidel
-
AFNI Message Board
hi Floris
One thing you could try is simply using 3dDeconvolve -nodata as you normally would but add in a censor file (via -censor) to censor out "volumes" where no data will be collected. Then, when you actually go to run the GLM on your data you can simply copy in volumes to the data you collected as placeholders when you run 3dDeconvolve so that the regressors generated by -stim_
by
jkeidel
-
AFNI Message Board
hi
at least with my afni_proc.py output there is a script in the results directory called @ss_review_basic that gives this information--for instance, from one of my participants towards the end of the output of the script (this is for RSA so I have 32 different stim classes):
TRs censored : 21
censor fraction : 0.020588
num regs of interest : 32
num TRs pe
by
jkeidel
-
AFNI Message Board
Page 1 of 3
Pages: 123