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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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Of course! Thank you, and thanks for taking the time to demonstrate how to answer the question for oneself, even if it feels a little bit obvious in retrospect (and so might have seemed like a silly question).
~j
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jflournoy
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AFNI Message Board
Thanks for your help. I may try that since I haven't hear from Bob or Rick.
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jflournoy
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AFNI Message Board
As the overly-verbose title says, I'm wondering if someone can confirm for me the column order in the x1D file if one uses a convolution with multiple basis functions and stim_times_IM.
3dDeconvolve -input ${FUNC} -mask ${MASK}
-num_stimts 1 \
-stim_times_IM 1 times.1D 'SPMG2(18)' -stim_label 1 Task \
...
For a simple example, say I have a stim_time
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jflournoy
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AFNI Message Board
Yes, I am using the -mask option though I forgot to include it in the original email. Thank you for making sure!
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jflournoy
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AFNI Message Board
Hi Gang,
I would like to follow up to ensure I'm doing this correctly. For my model, I'm permuting the data (I won't get into the specifics here) and generating one whole-brain Z-statistic map per permutation. As a start, I've generated maps from 2000 permutations, and then 3dTcat'd them into a 4d nifti. I'm then running 3dClustSim. For example:
3dClustSim -ath
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jflournoy
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AFNI Message Board
Thank you, Gang.
That is very helpful to hear. We are also producing maps from the group-level models estimated on permutations of our data as well to use with the -inset option in 3dClustSim as a baseline for comparison to the simulations using the acf estimated from the first-level data. Hopefully this confirms that intuition!
~John
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jflournoy
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AFNI Message Board
Hi AFNI folks,
Thanks for helping me think through this. In standard practice, we use 3dFWHMx to estimate the ACF parameters based on the residuals of the first-level "fixed effects" model. If we are, say, using SPM or FSL, we do this for each participant's first-level model and take the average (or median) ACF parameter to use in the 3dClustSim step. I think I have a tenuous un
by
jflournoy
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AFNI Message Board