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 - 24 of 24
Hello again!
I have a follow up question regarding the mask. I apologize if this is obvious answer, but I want to confirm so I can also accurately pass this information along to labmates with similar questions.
If our data were collected with a larger voxel size (e.g., 3x3x3) and resampled to 2x2x2, would I want my mask to match the resampled voxel size or original FOV voxel size?
Thank
by
jef
-
AFNI Message Board
Thank you so much! This is incredibly helpful! I too was surprised it ran without a mask.
by
jef
-
AFNI Message Board
Thanks for your reply and sorry I missed your replies.
Here is what I was running originally
# Set path to the RX directory to save output
rx_path=/nas/longleaf/home/jess1/whole-brain-dev-social/analysis/thresholding
# Set path to the mask used in analyses #mask is at 70% threshold grey matter mask
mask=/nas/longleaf/home/jess1/whole-brain-dev-social/thresholding/group_mask_acrosswave
by
jef
-
AFNI Message Board
Hello!
I'm trying to make sure I'm understand how the different parts of how 3dclustsim works.
I noticed if I don't specify a grey matter mask (i.e., no mask flag) in my 3dclustsim analysis, my k values are much lower. Intuitively, I would have expected the opposite. My goal is to include the whole brain in my calculation.
Could you help tease apart why my values vary so d
by
jef
-
AFNI Message Board
I have related question to the one above.
I'm trying to make sure I'm understand how the different parts of how 3dclustsim works since I'm using with first level models runs in spm.
Note: I've calculated my acf parameters from the first level residuals to ensure I'm not calculating acf parameters from residual files of my stats model at rx level.
I noticed if I
by
jef
-
AFNI Message Board
Hello,
I am trying to rerun my 3dlmer models with the bounds inclusion to make sure my results were not influenced by outliers, but I'm receiving the following error:
Here is the top of my script. Only edit is the "bounds" line
3dLMEr -prefix rec_3dLMEr_age2c_bounds -jobs 28 \
-model 'Rec*age_c+Rec*age2_c+(age_c|Subj)' \
-qVars "age_c,age2_c" \
by
jef
-
AFNI Message Board
Hi Gang,
This answers my questions!
Yes, my gender was indeed a factor, not binary 0/1.
Thank you so much!
by
jef
-
AFNI Message Board
Hello,
I've successfully implemented 3dlmer for longitudinal models where I've include both an age and age2 term (continuous, quantitative measure) and assessed gender differences (binary 0/1 coding).
3dLMEr -prefix 3dLMEr_age2_gender -jobs 28 \
-model 'task*age*gender+task*age2*gender+(age|Subj)' \
-qVars "age,age2" \
-qVarCenters "0,0" \
by
jef
-
AFNI Message Board
Hi Gang,
Thank you so much for your response.
I have a clarification question. If my goal is to compare the average of happy and sad conditions to the neutral condition, is it correct to specify 1*happy 1*sad -2*neutral?
Specifically, my goal is to have emotion (average of happy and sad) to be weighted the same as neutral.
Thanks again for your help!
by
jef
-
AFNI Message Board
Hello,
I have a related question. I am trying to better understand the differences between a few weight options.
I have a similar contrast in which I originally specified
1*happy 1*sad -2*neutral (emotion - neutral contrast is the goal)
Would it be equally correct to do
1*happy 1*sad -1*neutral
if the weights do not need to add up to zero?
I tried it out to see if the r
by
jef
-
AFNI Message Board
Thank you so much!
I'll dig into these resources to see how much this matters, but one thing I forgot to specify is that these are for data where the first level models were run in spm, so our files are .nii.
(I know the spm-afni combo is a larger topic for 3dclustsim in general, but we are already making sure acf parameters are being calculated from first level residuals, then averag
by
jef
-
AFNI Message Board
Hello,
I feel like this is fairly straightforward thing to do, but I also don't see much discussion around the different options of how people do this and how these decisions could impact thresholding estimates.
For a whole brain 3dclustsim thresholding calculation, do you have recommendations on how to calculate the group average mask? For example, do you recommendations on if and whi
by
jef
-
AFNI Message Board
Thank you, Gang!
Sorry I didn't see your reply earlier. This is really helpful.
I think part of my remaining confusion is rooted in whether when I change the value of quantitative variable in the model if I am changing my interpretation in the slope or the intercept.
For example, would it ever be appropriate to rerun the model age (or another centered quantitative variable) at dif
by
jef
-
AFNI Message Board
I plan to use 3dlme for a longitudinal (3 time point) fMRI study and I've reviewed the documentation and I've heard about the benefits of doing this quite a bit, but I'd love to check my logic in some of the specifics of how
1) I could model the data to assess how task activation changes across age and how a co-variate collected at time 1 may moderate this relationship
2) how I w
by
jef
-
AFNI Message Board
Thank you! I have a follow up question. I successfully ran the script with a small batch of participants, but when I try to run it for all subjects, I receive the error
[1] "Great, test run passed at voxel (30, 54, 45)!"
[1] "Start to compute 91 slices along Z axis. You can monitor the progress"
[1] "and estimate the total run time as shown below."
[1] "
by
jef
-
AFNI Message Board
I actually just caught another error that is now allowing the program to run!
I had indicated "Inputfile" instead of "InputFile"
Thanks for all your help in fixing all the other errors I had prior to this typo!
by
jef
-
AFNI Message Board
Thank you!
I fixed the qvars to only indicate one centered variable and updated my model name to indicate table-level variable names only. I also deleted variables from the table that weren't called in this simpler model in case that was also causing an issue?
I have a couple follow up questions. In the past using 3dLME, I had conditions specified under the table name (e.g., "Ant
by
jef
-
AFNI Message Board
At first I received an error when I ran require(data.table) indicating it could not be found and I was unable to download data.file, but I was able to install it with the command
install.packages("data.table", type = "binary")
Now my output is:
> require(data.table)
Loading required package: data.table
data.table 1.12.8 using 2 threads (see ?getDTthreads). L
by
jef
-
AFNI Message Board
Thank you! The error is resolved now when I run the afni_system_check.py.
However the script will not still not run. A new command line appears immediately and nothing is produce, including no error.
I've ensured bash scripts run properly, that the script is executable, that I'm in the correct directory to run the script. I've confirmed R and afni are both loaded.
Is there so
by
jef
-
AFNI Message Board
Hi,
Yes, here is the full output. Additional information that may be helpful is that we just updated our software to Catalina on our Mac.
Thank you!!
-------------------------------- general ---------------------------------
architecture: 64bit
system: Darwin
release: 19.6.0
version: Darwin Kernel Version 19.6.0: Mon Aug 31 22:12:52 P
by
jef
-
AFNI Message Board
Hello,
I am trying to run 3dLME on our local lab mac machine that has had various versions of afni installed on it throughout the years. I recently updated the software to allow for needed R version and packages to be installed and updated our afni binaries. I also updated all other programs, such as homebrew, xcode, and x11. When I run the code, it doesn't produce an error, just returns
by
jef
-
AFNI Message Board