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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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I am using 3dLME to test some group x time interactions in a longitudinal dataset. The data has 2 groups (TMS v. Sham) and 5 time points (wk0, wk1, wk6, wk7, wk12), but a lot of subjects have missing time points.
I would like to run the overall model with all time points (time as a categorical variable), but then use contrasts to test the group x time interaction for specific pairs of timepoi
by
wsen
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AFNI Message Board
I have task-based fmri data that has been processed in fsfast, as well as resting state data preprocessed with fmriprep, and then smoothed and denoised using the CONN toolbox. For both of these data sets, I would like to use the output (contrast estimate files for the task based, and fishers Z connectivity maps for resting-state) to do group analysis using 3dLMEr, and then use FWHMx -ACF and 3dCl
by
wsen
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AFNI Message Board
For anyone who comes across this thread in the future, Gang Chen let me know that the script worked fine when he tried it, suggesting that the problem may have something to do with the computing cluster I am using.
Thanks again for looking into that!
by
wsen
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AFNI Message Board
I have uploaded a tar.gz with the script and data to:
The output from running the script with and without the mask option are also included in this folder (For the one without the mask option, I aborted once I saw that the slices were being processed, as it was only a test run).
Let me know if another format is better for you.
Thanks
Walker
by
wsen
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AFNI Message Board
Hi AFNI experts,
I am running 3dLME on high resolution data that only covers a portion of the brain. I am using the -mask option to reduce the time and resources it will take, using this command:
3dLME -prefix Rest_LME -model "Cond*Side" \
-ranEff "~1" -SS_type 3 \
-jobs 6 \
-mask ./groupmask_all+tlrc \
-num_glt 6 \
-gltLabel 1 'Threat m Safe' \
-gltCod
by
wsen
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AFNI Message Board
I modified Dr. Cox's script for my data and it seemed to work well, but that is good to know about the unWarpEPI.py script for future use.
Thanks to both of you!
by
wsen
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AFNI Message Board
That would be really great, thank you! Can you attach it here, or would you like my email address?
Thanks!
by
wsen
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AFNI Message Board
Fair enough. I really just meant to ask whether you would consider -plusminus a reasonable way to do reverse PE correction, or if it is more of a first step toward AFNI supporting this type of distortion correction. In the help for 3dQwarp it says that this type of correction is "one goal" of the -plusminus option. I wasn't sure if that wording indicated that this idea is sort of
by
wsen
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AFNI Message Board
Hi AFNI experts,
I have some 7T fMRI data with short reversed PE scans that I would like to use for distortion correction. I was hoping I could get some opinions about the best way to go about this. I know 3dQwarp's -plusminus option can be used for this, but (from a novice perspective) this seems like a less sophisticated approach than something like FSL's topup, which uses informa
by
wsen
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AFNI Message Board
Hi Bob,
Thanks for the information. That makes sense. I hadn't noticed that some messages start with "warning" and others "error" - that is a good distinction for me to be aware of.
by
wsen
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AFNI Message Board
Afni experts,
I am getting the following set of errors running afni proc.py on a subject:
*+ WARNING: Smallest FDR q [2 NE#0_Tstat] = 0.999899 ==> very few (if any) true detections
*+ WARNING: Smallest FDR q [4 NE#1_Tstat] = 0.999897 ==> very few (if any) true detections
*+ WARNING: Smallest FDR q [6 NE#2_Tstat] = 0.780828 ==> very few (if any) true detections
*+ WARNING: Smalle
by
wsen
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AFNI Message Board