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 - 16 of 16
Hi all,
I have a 2 group by 2 condition mixed effects analysis, and want to test for a group by condition interaction. The groups have unequal numbers of subjects. Although I don't personally have a problem with Gang's notion of testing for differences between each group's condition contrasts to get the interaction (i.e., Group1(Cond1-Cond2) - Group2(Cond1-Cond2)), some collabor
by
Thomas
-
AFNI Message Board
Hi all,
I really like the idea of using the -ortvec input option to more simply define stuff like motion parameters in the baseline model of a 3dDeconvolve GLM. However, in my output bucket images, I get buckets pertaining to every regressor included in -ortvec, including fstats and tstats if I had indicated so. I'm not interested in looking at the maps associated with those baseline regr
by
Thomas
-
AFNI Message Board
Hi all, I am trying to install the necessary packages to run 3dMVM but cannot get the afex or phia packages to install.
--> rPkgsInstall -pkgs ALL
Warning messages:
1: In getDependencies(pkgs, dependencies, available, lib) :
packages ?afex?, ?lme4? are not available
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package 'phia' had non-ze
by
Thomas
-
AFNI Message Board
Hi All,
Do you know if anybody has published on the global connectivity index as measured by 3dTcorrMap? I'm wondering under what contexts it has been applied and what sorts of questions previous researchers have answered with it. It seems like an interesting metric, and it appears to nicely corroborate some connectivity analyses I am working on, but I wonder how it is received by the fie
by
Thomas
-
AFNI Message Board
Hi all,
I wish to analyze the aplitude spontaneous oscillations at multiple frequency ranges as done in Hong 2013. Can this be done with 3dRSFC? Do I set the bandpass frequencies as my desired range? Also, how might I set a high-frequency cutoff?
3dRSFC -no_rsfa -mask ${refdir}/minicolin+orig -nodetrend -blur 6 -band .01 .05 -prefix ${id}_LF grptransrest+orig
3dRSFC -no_rsfa -mask ${refdir
by
Thomas
-
AFNI Message Board
Oh, I need to center the subjects' brain maps with each other on a voxelwise basis?... this is going to be harder than I thought now...
by
Thomas
-
AFNI Message Board
Thanks - would not have thought of that! Do I need to center x and y before starting step 1?
by
Thomas
-
AFNI Message Board
Yes, I believe so! The a3*X*B is the interaction term I'm interested in for the moderator analysis, but I'm not sure how to code it when B is brain.
by
Thomas
-
AFNI Message Board
Hi all,
I wish to perform a moderation analysis where brain moderates the relationship between two continuous between-subject variables. How can I do this with the AFNI suite? I know I can use a combination of 3dttest++ and 3dRegAna to do mediation analysis (brain as mediator) but I'm not sure about moderation. I have a hunch that 3dttest++ might do the trick - if this is the case, what
by
Thomas
-
AFNI Message Board
Hi everyone,
I have what I hope to be a pretty simple question. If I list include a set of regressors in my 3dRegAna xydata lines but don't reference them in the model at all, are they completely ignored in the analysis? Or, do they need to be excluded from the whole regressor matrix in my code in order to be ignored?
Thanks!
Thomas
by
Thomas
-
AFNI Message Board
Hi all,
I have a two questions about performing a regional homogeneity analysis.
1. Is it best to smooth before or after ReHo? I've found examples of smoothing first (Wu 2008; Yao 2008 ) and, alternatively, ReHo first (Liu 2010; Shukla 2010).
2. I have found some papers in which individual KCC maps were normalized via dividing by a mean KCC value. But I'm not sure whether to
by
Thomas
-
AFNI Message Board
Gang, thanks again for your assistance.
Actually, the 4th column is an alternative explanatory variable in lieu of my original one. I had thought that if I include it in my script but not reference it in the model, then there would be no harm. I hope that's the case!
The 5th column t-stat does seem generally in line with the whole model F-stat, although I haven't tested 5: 0 1 2
by
Thomas
-
AFNI Message Board
Hi Gang,
Here's the important stuff in my script:
3dRegAna -rows 63 -cols 5 \
-xydata 5.66154 1 0 0 12.2829 ./5406_Z+orig \
-xydata 8.66154 0 0 0 -0.5771 ./5407_Z+orig \
-xydata -2.33846 0 0 0 4.3129 ./5408_Z+orig \
......
-model 5 : 1 2 3 0 -bucket 0 reg
I did center variable A, even though it is a change score (col 5). Age (col 1) was also mean-centered and the other covaria
by
Thomas
-
AFNI Message Board
Hi Gang,
Variable A has the same average value across gender and age groups. I'm only interested in the effect of variable A, but if I'm reading my output correctly then one of my covariates (scanner - data collected on two scanners) may be contributing an effect on this cluster above and beyond my variable A?
Thomas
by
Thomas
-
AFNI Message Board
Hi all,
I have a few questions about two separate problems.
Firstly, I have a regression analysis I'd like to solve. It involves one explanatory continuous variable (A) and two categorical (age, sex, coded as 0/1) & one continuous (B) covariates. My model would be the following, correct?
-model (A) : (age) (sex) (B) 0 -bucket 0 ${output}
Now, in my output, the F-stat and R
by
Thomas
-
AFNI Message Board
Hi all,
I am hoping to try using ANATICOR with some resting-state data. The data has already been despiked slicetimed and volregged, but instead of motion 1D files I only have .txt files. Is there an easy way to convert these to 1D files and preserve their column formatting?
Additionally, does anybody have experience segmenting via FAST instead of FreeSurfer? I'm curious how the pre
by
Thomas
-
AFNI Message Board