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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
History of AFNI updates
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Thanks Paul! Yea I was using it on the afni_proc.py output, but I don't use the tlrc option in my scripts (I keep everything in native space for my analyses). I used the 3dGrayPlot program but I like that the @grayplot program plots the motion parameters and censored volumes.
Thanks again for making this program--very useful!
Best,
Kate
by
katemills
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AFNI Message Board
Thanks Paul!
The code still created an error for me, and I realized it was because my data are in orig space, and @grayplot is hardcoded to expect +tlrc in the image files. So I changed that and the program worked--thank you again!
Best,
Kate
by
katemills
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AFNI Message Board
Dear AFNI wizards,
I tried using @grayplot and was encountering errors (unable to read the directory), so I updated my afni binaries (Precompiled binary macos_10.12_local: Jul 31 2018 (Version AFNI_18.2.06)) and now the program @grayplot is gone. Is it really gone? Will it return one day?
Thank you,
Kate
by
katemills
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AFNI Message Board
Hi Gang,
Thanks again for all your feedback and adding these options. I am curious to know if 3dLME is fit using REML or ML. I ask because I believe that if we want to compare the loglik, AIC, or BIC for models with different fixed effects, it is required that they were fit using ML, whereas the default for lme is to use REML.
Thank you!
~DSN Lab
by
katemills
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AFNI Message Board
Hi Gang,
That is great news. I think people would be well served by also being able to easily retrieve AIC and BIC as well.
Thanks!
UO Developmental Social Neuroscience Lab
by
katemills
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AFNI Message Board
Hi Rick,
Thank you so much for your input. We have the added difficulty that we're doing most of our analysis in SPM.
1. Our residuals file is from the group-level model from SPM -- ResMS.nii is the map of mean squared residuals. This is why we believe we have to take the square-root. Sounds like that's consistent with what you're saying.
2. So, because our residual file
by
katemills
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AFNI Message Board
Dear AFNI community,
This question is related to previous posts from earlier this year:
In short, we want to double check that we are using the proper inputs to 3dFWHMx, particularly regarding the -acf and -detrend flags.
1. Our understanding is that AFNI expects residuals to be standard deviations, so we are square rooting the residuals. Can we confirm that this is what the function
by
katemills
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AFNI Message Board
Hi Gang,
Thank you very much for the advice. Running this command alerted us to the fact that we were missing the "afex" and "paran" packages. I didn't see either of those packages listed as dependencies on the 3dLME help guide, but since it's running now, looks like they were necessary nonetheless.
Thank you again for your help and for your quick response!
by
katemills
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AFNI Message Board
Hi there,
I'm attempting to use 3dLME to model the interaction between two within-subject categorical variables and the linear and quadratic effect of age (this is a longitudinal study). When running the following model without specifying contrasts, it is estimated without problem.
3dLME -prefix SelfOverTime_3Ts -jobs 8 \
-model "target*domain*age_c+target*domain*age_c2"
by
katemills
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AFNI Message Board
Hi All,
I was wondering if RetroTS is able to handle Siemens PMU files (i.e., .resp and .puls logfiles)? I have seen previous posts where it appears people have used these files at their input data files, but also posts where individuals have converted these files into 1D files. However, I am unsure as to how these conversions were done. Any suggestions would be greatly appreciated!
Thank y
by
katemills
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AFNI Message Board