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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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You can theoretically take either betas or correlation coefficients to the group level (though in the case of the latter, you would probably want to z-score). As I understand it, it is more common to do group statistics over individual subject betas. See the bold text in Gang's post here:
Regarding the issue of understanding directionality, I've used the approach you describe (3dmas
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zreagh
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AFNI Message Board
Thanks for the reply! I actually have not tried that - thank you for the suggestion. Will report back in a day or so.
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zreagh
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AFNI Message Board
Hi all,
I'm no stranger to troubleshooting alignment woes, but this is a particularly frustrating case, and I welcome any tips.
I have a dataset with about 15 T1w structural images and ~80 resting state EPIs (same brain). The T1w image is more or less AC-PC, whereas the EPIs are extremely oblique. Long story short, the align_epi_anat.py segment of my afni_proc.py pipeline is not having
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zreagh
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AFNI Message Board
Hi,
Quick question regarding the output of 3dLSS using single-trial betas via the stim_times_IM option in 3dDeconvolve. In general, the resultant dataset appears to have twice the number of subbricks as there are discrete stimulus time points. In other words, if my stim times file contains 12 time points, the dataset generated by 3dLSS has 24 subbricks. Unfortunately, the subbricks are not bei
by
zreagh
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AFNI Message Board
Hey Rick,
Thanks so much for your help and for adding the fix to timing_tool.py!
Best,
-Zach
(EDIT: just re-ran after updating binaries and it worked without a hitch. Thanks again.)
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zreagh
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AFNI Message Board
In case anyone happens to see this, I've ascertained that 3dDeconvolve will run. It's only 3dREMLfit where I'm encountering this problem.
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zreagh
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AFNI Message Board
Hello,
I'm running afni_proc.py on a dataset and am consistently encountering a problem when it gets to the timing_tool.py step for 3dREMLfit (I am skipping 3dDeconvolve once the design matrix has been generated). In particular, here is the error I'm getting:
timing_tool.py -multi_timing stimuli/stimTimes_1.1D stimuli/stimTimes_2.1D stimuli/stimTimes_3.1D stimuli/stimTimes_4.1D st
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zreagh
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AFNI Message Board
Hi Rick,
Thanks so much for the reply. I tried doing that, but the script threw a few errors related to missing tlrc options. I probably wasn't particularly careful with modifying the rest of my call! I'll give it another go.
One more related question, if you get a second: let's say I wanted to use the tlrc option, but would also like to be able to view my statistical maps in
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zreagh
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AFNI Message Board
Hi,
I am presently optimizing a version of the afni_proc.py call for use in my lab. I have a quick question regarding template space.
In a nutshell, I am wondering if it is possible to run through the entire pipeline retaining the original subject's space (all steps, including alignment and regression) rather than Talairach space. Apologies if I missed this in the documentation, but I
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zreagh
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AFNI Message Board
Hello,
I've recently moved over to trying afni_proc.py as opposed to my home-brewed preprocessing pipeline. I'm having an interesting issue with EPI-to-structural alignment. For some background, structural is 0.75mm isotropic and EPI is 1.8x1.8x2.0mm. The EPI is a partial volume with axial slices that covers from roughly the bottom of the temporal lobe to just above the apex of the c
by
zreagh
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AFNI Message Board