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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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Hi Gang,
Collinearity is very high. Several regressors have VIFs greater than 10. Whereas the model created by 3dLSS at each iteration has VIF less than 2.
Anyhow, 3dLSS did work after I downsampled the timeseries data from 250Hz to 10Hz.
Thank you,
Chirag
by
chirag90in
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AFNI Message Board
Hello,
I am trying to run 3dLSS on a 1D timeseries data. The timeseries is of size 5MB, and the design matrix is of size 179.4 MB. When I try to run 3dLSS I get the following error:
0m malloc failure for image space: 2904614976 bytes
I also tried running it by requesting more memory, but it still kept giving me the same error. Is there a solution to this?
Thank you,
Chirag
by
chirag90in
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AFNI Message Board
Hi,
I had tried that solution earlier, but it did not work for me. Thank you though
by
chirag90in
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AFNI Message Board
Hi,
install.packages("brms") still gives me the same error as that I originally posted. My system check looks as follows:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 3.10.0-957.1.3.el7.x86_64
version: #1 SMP Thu Nov 29 14:49:43 UTC 2018
distribution:
by
chirag90in
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AFNI Message Board
Hello Mr. Taylor,
Thank you for your reply.
I am using CentOS 7. Following is the output for afni_system_check.py -check_all:
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 3.10.0-957.1.3.el7.x86_64
version: #1 SMP Thu Nov 29 14:49:43 UTC 2018
distribution:
by
chirag90in
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AFNI Message Board
AFNI experts,
I am trying to install R's brms package so I can use the newly introduced afni function RBA. Following the installation step mentioned in RBA documentation, I tried to install the brms package using the following command: rPkgsInstall -pkgs "brms" -site ";.
However, I got several errors (see below). Any help in order to fix this problem will be highly appre
by
chirag90in
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AFNI Message Board
Hi Gang,
I am playing around with some held-out data and the sample size is too small (N = 10) to do random-effects analysis.
Thanks,
Chirag
by
chirag90in
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AFNI Message Board
Hi Gang,
Is there another way to carry out fixed effect analysis across multiple subjects without using all-subject concatenated data in 3dDeconvolve/3dREMLfit?
Reading your post I understand that I will have to run regression by concatenating all subjects' data. However, I already have effects estimates for every subject from running 3dDeconvolve on them individually. I was just wonde
by
chirag90in
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AFNI Message Board
AFNI Experts,
I am trying to install afni on my linux (CentOS 7). I am getting many warnings and error messages when I try to install R (using rPkgsInstall -pkgs ALL). Is there a solution for the following error?
Error: package or namespace load failed for ‘RCurl’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/lceuser/R/RCurl/libs/RCurl.so':
li
by
chirag90in
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AFNI Message Board
Gang,
I am not sure if I can do that, as my pairing is not between different conditions but it’s between different groups. For example, pairing between pre and post treatment groups.
Thanks,
Chirag
by
chirag90in
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AFNI Message Board
Hi Gang,
We are using 3dMEMA to run a paired t-test. There is not much documentation on how to do a paired t-test in 3dMEMA, but I looked at the documentation of 3dttest++. It mentioned two ways for doing a paired t-test: I can either provide the paired subjects as separate sets, or I can provide a single set in which each input is the beta difference of the pair.
I think I have to use the
by
chirag90in
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AFNI Message Board
AFNI Experts,
I am carrying out "denoising" (using ICA AROMA) separately on each run of the functional dataset. This denoising produces several components (timeseires) which represent noise for that particular run. I want to include these timeseires as confounds in my 3dDeconvolve model. However, since each run may have different number of confound timeseries, I cannot put them in on
by
chirag90in
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AFNI Message Board
Clarification: the two groups have different sets of subjects, i.e, “paired” subjects A1 and B1 are not the same subject. You still think paired t-test is the only way?
Thank you
Chirag
by
chirag90in
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AFNI Message Board
Thank you, Gang.
Yes, there are exactly same number of subjects in each group like you understood; A1 paired with B1, A2 with B2 and so on...
by
chirag90in
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AFNI Message Board
AFNI Experts,
We have two groups of subjects. Each subject from one group is paired with a subject from another group in the sense that they performed the same task with a slight variation. We are interested in modelling the paired difference between them as well as estimate subject effects. I don’t think using a paired t-test as in a typical within-subject design is appropriate. What will be
by
chirag90in
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AFNI Message Board
AFNI Experts,
Is it recommended to use the whitened residuals (-Rwherr) to estimate cluster size (in 3dclustsim)?
Thank you
Chirag
by
chirag90in
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AFNI Message Board
Thank you.
What is the process for prewhitening the resting state data?
by
chirag90in
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AFNI Message Board
Thanks, Gang.
I was wondering if there was a way to just prewhiten the data and avoid running regression analyses. The 3dREMLfit, after prewhitening, also carries out regression analysis and produces betas.
I am looking for a way to just prewhiten the data.
Thanks,
Chirag
by
chirag90in
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AFNI Message Board
Hi,
I used the 3dRELMfit to perform prewhitening. Although 3dREMLfit allows to output both non-prewhitened and prewhitened residuals (-Rerrts and -Rwherr), it produces betas weights from the REML (prewhitened data) estimation only, right?
Also,
I there any other way besides using 3dREMLfit to independently prewhiten the data? I want to avoid running the GLM analysis.
Thanks
Chirag
by
chirag90in
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AFNI Message Board
AFNI experts,
The 3dDeconvolve saves the full model design matrix. I was wondering if there was a way to also save a similar design matrix (with same formatting, including the # headers) that includes only the stim_times timeseries?
Thank you,
Chirag
by
chirag90in
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AFNI Message Board
AFNI Experts,
Is there a recommend number of decimal places to be used for the onset (or duration) times in the stim text files?
Thank you
by
chirag90in
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AFNI Message Board