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 - 17 of 17
Hi AFNI experts,
This is a trivial (but annoying) problem that I am sure has a very simple solution, and yet I cannot find it . Whenever I switch the underlay (to the anatomical image) in afni viewer, it also changes the overlay; and when I change the overlay (to a functional image), the underlay also changes. Previously, I was able to separately select underlay (as anatomical) and overlay (as
by
dani2
-
AFNI Message Board
Hi AFNI experts,
I am running a gPPI analysis similar to what is described here (https://afni.nimh.nih.gov/CD-CorrAna). The task is a simple n-back task, so I have separate PPI interaction regressors for 2-back and 0-back, respectively, on the first level. The study is an intervention study with an experimental arm and a control arm, so I am assessing for a group x time intervention in the gro
by
dani2
-
AFNI Message Board
Thank you! I have been able to get my post-fmriprep processing pipeline to work well. However, now I have a related question. I am using 3Dclusterize to list clusters over a certain threshold, and I would like to list them in MNI space. I have read on another thread (https://afni.nimh.nih.gov/afni/community/board/read.php?1,161972,161980) that 3dclusterize is supposed to know whether your data ar
by
dani2
-
AFNI Message Board
This indeed solves the first error - thank you for that! And now I am left with the other two. I am not sure if these are related to installation of AFNI and version of R? When I installed AFNI, I already had two versions of R on my workstation, one that I use regularly (R 4.0.3 in /usr/bin/R) and another one (R 3.6.3 in /opt/R/3.6.3/bin/R). I assumed AFNI was using the R in my path (which R=/usr
by
dani2
-
AFNI Message Board
I am trying to run 3dLMEr to assess group*time interaction effects in an n-back task in an intervention vs. control group. (I am using 3dLMEr because I have within-subject quantitative covariates - FD and accuracy - that I would like to adjust for.) I previously had 3dLME up and running on another environment, but I have R 4.0.3 on this workstation, so it has been a challenge. I updated all of th
by
dani2
-
AFNI Message Board
I apologize for being rather vague! This would be for a task-based analysis. fmriprep yields preprocessed files along with a .tsv file of nuisance regressors. Ideally, I would like to implement something like Example 6b, but starting after blur:
afni_proc.py \
-subj_id FT.e6b \
by
dani2
-
AFNI Message Board
Hello experts,
I have preprocessed my data using fmriprep. However, for first and second level processing I would like to use AFNI. (I have historically used SPM, but am switching to AFNI for a number of reasons, namely flexibility of second level models, ability to see the data, cluster algorithms for multiple comparisons - so I am relatively new to AFNI.) I am wondering if it is possible to us
by
dani2
-
AFNI Message Board
That's great! And just to confirm, 3dLMEr runs well with R 4.0 versions, correct? (I know there were problems with 3dLME.) Also, do you have an estimate of when this will be available, and if there will be a notice sent out when this is released? Thanks so much!
by
dani2
-
AFNI Message Board
Hello,
I was wondering if any more progress had been made to implementing the "residuals" option in 3dLMEr? This was brought up in the following thread a few months ago (https://afni.nimh.nih.gov/afni/community/board/read.php?1,162874,163747#msg-163747), but I know how things get busy! - and I see the option is still commented out in github. I updated R to 4.0 and now 3dLME will not ru
by
dani2
-
AFNI Message Board
Just in case this is helpful to anyone else...
Thank you Gang! Your advice to switch the order of my continuous and categorical variable in the gltcode worked, so that categorical was first and continuous was second, like this. The program was crashing when the continuous variable (Negurg_mc) was first and categorical variable (Task) was second.
-num_glt 9 \
-gltLabel 1 'rsFC' -gl
by
dani2
-
AFNI Message Board
Could you show the contingency table about Task and Gender? You can find it on the terminal when you run your 3dLME script.
I actually do not see this. The output includes:
++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
107 subjects : 10170 10181 10183 10185 10186 10187 10190 10192 10193 10194 10196 10198 10200 10201 10202 10203 102
by
dani2
-
AFNI Message Board
Update: I was getting the same error message with 3dLME because a few syntax errors had sneaked in the gltcode. But now that those are corrected, the packages have seemingly loaded correctly, the program is still hung up at the point of:
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 inappropri
by
dani2
-
AFNI Message Board
I have installed R 3.6.3 and re-installed all of the packages, and I unfortunately am still getting the same error messages.
I also thought that I would try the new version (3dLMEr) and there I am getting the error message that 3dLMEr: command not found (even though I installed this package, along with "phia" and "snow"), which makes me think that afni is not "seeing&
by
dani2
-
AFNI Message Board
And I apologize - I realize I did not answer the rest of your question! I am running on Ubuntu 18.04.
Also, I did get the following message when I attempted to install the packages in R, as I am running this on a shared server (and R is installed in a read-only directory):
Installing package into β/software/R/3.5.1β
(as βlibβ is unspecified)
Warning in install.packages("nlme")
by
dani2
-
AFNI Message Board
We are running R version 3.5.1. I can try to upgrade to version 3.6 to see if that would help?
by
dani2
-
AFNI Message Board
Hello -
I am running 3dLME to assess whether PCC functional connectivity changes across task (within-subject); correlates with a between-subject continuous variable of negative urgency (Negurg_mc); and whether there is interaction between the two. I wanted to use 3dMVM, but I have a mean framewise displacement measure for each task, which would be a within-person continuous variable, so I think
by
dani2
-
AFNI Message Board