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 1 Pages: 1
Results 1 - 12 of 12
Thanks Paul, this makes a lot of sense. Luckily it means all my code is actually correct, I just have to adjust when I visualize. A great outcome!
by
rwaugh
-
AFNI Message Board
Hi Paul,
Thank you for the detailed response. After investigating this a little more, I see that I have conflated two separate issues. With the example I gave above, the two actually are pretty much identical (though I take your point on the wisdom of using bisided vs. 2sided). Embarrassingly, I think the discrepancy I saw was because I checked the "pos" button and thought I was mis
by
rwaugh
-
AFNI Message Board
Hi there,
I am trying to understand something about 3dClusterize. This is my code:
3dClusterize \
-inset file.nii \
-mask mask.nii \
-ithr 9 \
-idat 8 \
-NN 1 \
-2sided p=0.001 \
-clust_nvox K \
-pref_map tmp_output.nii
It works as I expect except that when I compare the cluster map to the manual version of looking at the same file (setting the threshold to p < 0.001 with mi
by
rwaugh
-
AFNI Message Board
Ah, yes! That is exactly what I want. I've been using AFNI for years and never noticed those A/B boxes before Thanks so much!
by
rwaugh
-
AFNI Message Board
Hi, Thanks for getting back to me so quickly. I have a network mask (in grey) and the colored areas show voxels that are significant for a contrast within the network. We want to show which areas of the brain are included in the network referenced against the results of the statistical test. My colleague tells me there may be a way to do this in photoshop so I might migrate the images over there
by
rwaugh
-
AFNI Message Board
Hi All,
Hoping for some aesthetic assistance with a brain image. I am trying to create an image with a semi-transparent background for part of the overlay image and non-transparent for the rest of the overlay. Is there a way to do this with the AFNI viewer? (I know you can control the transparency of the overlay as a whole, but I just want to do part of it). I am attaching an example image, w
by
rwaugh
-
AFNI Message Board
Hi there,
I am using a linear mixed effect model to test some data within a series of 6 of network masks. It is the exact same model/type of data/number and proportion of conditions and subjects, just different networks. The model works correctly for 5 of the masks, but for some reason hangs at this step for the sixth mask:
"If the program hangs here for more than, for example, half a
by
rwaugh
-
AFNI Message Board
Hi Gang,
Thanks for the response. I've been reading your comments on the other thread about issues with treating the corrected p < 0.05 as a binary pass/fail. Your idea of "highlighting, not hiding", is especially helpful in framing how to consider and report these results (ie. looking at the broader range of thresholds).
Becky
by
rwaugh
-
AFNI Message Board
Hi there,
I know this topic has been covered before but I'm hoping for some help to make sure I understand all options for cluster thresholding after running 3dLME and/or 3dMVM.
So far, I have tried outputting the residuals then running:
3dFWHMx -ACF NULL -mask mask.nii -input residuals.nii -unif
3dClustSim -acf 0.34947 4.38785 11.4259 -mask mask.nii
(The mask is just a bin
by
rwaugh
-
AFNI Message Board
Thanks, that makes sense. I took a look at the ratio of instances of mixed scanner time points within subjects for both cases and in case B (hanging failure) ~13% of the subjects contributed mixed data while in case A, 25% of the subjects had mixed scanner within-subject, so perhaps that is the difference.
by
rwaugh
-
AFNI Message Board
Hi there,
I am trying to implement two analyses with the following longitudinal designs:
In case A, we have three measurements per subject (with some missing data) and the explanatory variables:
(1) ISI: time between measurements, W/S
(2) Age: age at baseline, B/S
(3) Cond: control or cond1, B/S
In case B, two measurements per subject and same explanatory variables (1) and (2) but
by
rwaugh
-
AFNI Message Board