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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
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As an update - I tried testing the model as follows:
1) Including Group+Sex (taking out MEdu) - This still failed (same error message).
2) Including Group+MEdu (taking out Sex) - This is working!
I think it might be because when I include Sex and MEdu as additional factors, the contingency tables look like this:
Contingency tables of subject distributions among the categorical variables:
by
janelleliu
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AFNI Message Board
Hello!
I'm encountering some issues with running 3dMVM where it will read the input files but throw the following error:
Reading input files now...
Reading input files: Done!
If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.
~~~~~~~~~~~~~~~~~~~ Model test failed! ~~
by
janelleliu
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AFNI Message Board
Hi Gang,
Thanks for the explanation re: internal dummy coding for 3dMVM - very nifty!
I will try using just one model for all of my hypotheses - but since I am not interested in modeling the interaction between Group and FatherAge (i.e., I just want to regress out the effect of FatherAge as a covariate of no-interest to control for it), would the following be appropriate?
-bsVars "
by
janelleliu
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AFNI Message Board
Hi Gang,
Thank you for the suggestion for 3dMVM - after reading through the documentation on 3dMVM, it does seem to be much easier for my situation. I wanted to make sure I understand - is the reason behind why dummy coding is not necessary for 3dMVM because the program can accept explanatory variables that are categorical (i.e., factors) in addition to explanatory variables that are quantitat
by
janelleliu
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AFNI Message Board
Hi Gang,
I have thought more about my research question and have a few follow-up questions that I hope to get some help on. For context: I have 2 groups (HR: high risk for autism; LR: low risk for autism) with an uneven number of subjects in each group. I'm interested in the difference in amygdala functional connectivity between the groups, as well as how Brain Volume (continuous variable
by
janelleliu
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AFNI Message Board
Hello!
I'm interested in running an unpaired t-test in 3dttest++ comparing functional connectivity (of amygdala ROI) between 2 groups while controlling for categorical (Site (4 levels), Maternal Education (3 levels)) and continuous (Father's Age) covariates of no-interest.
Based on this previous post, I have noted that categorical variables with two levels should be coded as 1/-
by
janelleliu
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AFNI Message Board
Hello!
I'm having trouble launching AFNI from terminal (running on macOS Catalina 10.15.6). When I try to launch AFNI by typing "afni -niml &" it will launch the initial AFNI display (initial window with license info and julian date, etc.), but it presents warnings (shown below) and does not launch the full gui. I've tried rebooting my computer and relaunching X11 as we
by
janelleliu
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AFNI Message Board
Hi Gang,
Thanks for the suggestions! I'll try out the first model and go from there.
Yes, VolRemaining is the number of TRs after censoring (scrubbing).
-Janelle
by
janelleliu
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AFNI Message Board
Hi again,
Another (follow-up) question about covariates. I am running ANCOVA using 3dMVM on seed-based resting state data with 3 between-subjects variables: "Group" (three groups; this is the variable of interest), "VolRemaining" (volumes remaining after scrubbing) and "Birthweight."
I'd like to incorporate both VolRemaining and Birthweight as covariates
by
janelleliu
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AFNI Message Board
Output of conda env list is:
# conda environments:
#
base * /Users/liuj10/opt/anaconda2
/usr/local/fsl/fslpython
/usr/local/fsl/fslpython/envs/fslpython
When I run grep -h "conda activate" ~/.*rc nothing is returned! Should I try a different file?
Output of cat ~/.condarc is:
ssl_verify: true
channels:
by
janelleliu
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AFNI Message Board
Hi, no worries - totally understand how things pile up quickly on the MB!
I believe I do have Xcode already installed ("which g++" returns "/usr/bin/g++").
I did the copy/pasting for the bash stuff, and also restarted my computer. After this, the output of "afni_system_check.py -check_all" is:
-------------------------------- general ---------------------
by
janelleliu
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AFNI Message Board
To follow up on my prior post - is there a way for me to change it so that AFNI points to the second instance of:
R (/Library/Frameworks/R.framework/Versions/3.6/Resources/bin/R)
python (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
python2 (/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7)
rather than using the anaconda versions of those pro
by
janelleliu
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AFNI Message Board
Oh yes, I should have specified - I have a few versions of R downloaded!
Output of that command is:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Thu Jun 18 20:49:00 PDT 2020; root:xnu-6153.141.1~1/RELEASE_X86_64
distr
by
janelleliu
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AFNI Message Board
Thanks for the help!
I was able to run the command successfully, but even after restarting the computer, it's still throwing the same error "R: Command not found." When I do "which R" it points to an anaconda R rather than R proper; I have R 3.6 downloaded, but is it possible that AFNI is trying to use the wrong R?
-Janelle
by
janelleliu
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AFNI Message Board
Hello!
I'm running into some issues with using R with AFNI on a macOS Catalina 10.15.6. The AFNI version I'm using (output of afni -version) is: Precompiled binary macos_10.12_local: Mar 30 2020 (Version AFNI_20.0.24 'Galba').
I'm trying to run 3dMVM and at first I got some error messages that said "Failed to load R_io.so with this error message," but bas
by
janelleliu
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AFNI Message Board
Masking afterwards in the 3dClusterize step worked well - thanks for the suggestion!
by
janelleliu
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AFNI Message Board
Hello again!
I've been running 3dMVM on seed-based resting state data using a bunch of different seeds and it is working for all of my seeds except two (L/R calcarine ROI), where it will read the input files but then throws the following error:
Reading input files now...
Reading input files: Done!
If the program hangs here for more than, for example, half an hour,
kill the pro
by
janelleliu
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AFNI Message Board
Re: centering, thank you for sharing the link! Based on the section "When to center within- or across-groups?" it seems like the overall idea there is to use centering to get rid of within-group variability in order to better examine between-group differences. In my case, the covariate of no interest is not linked to group status and my goal isn't to necessarily get rid of within-g
by
janelleliu
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AFNI Message Board
Hi Gang,
Thanks for your response!
Yes, VolRemaining does not vary within subject - thanks for pointing out that it should be a between-subjects quantitative variable. Is it still appropriate to specify that in the code with the -qVars "VolRemaining" option?
VolRemaining is significantly different between two of my groups (between CON and POME), so I want to covary for it to e
by
janelleliu
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AFNI Message Board
Hello!
I'm a little confused about specifying variables in 3dMVM when I have a quantitative covariate of no interest. My goal is to run a one-way ANOVA on some seed-based resting state data with 1 between-subjects variable, "Group" (3 groups: CON, POE, POME), and 1 within-subject variable "VolRemaining" (Volumes remaining after scrubbing), which is my covariate of no i
by
janelleliu
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AFNI Message Board