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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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gregetarian
March 02, 2023 10:45AM
Dear Gang,

I hope you're keeping safe and well.

I've been running a number of LMEs as follows. At risk of having totally missed something obvious, I think I've spotted an issue with the calculation of the z-score of voxels within post-hoc GLTs. For posterity, I'm detailing the issue here.

3dLME -prefix /data/gcooper/movie_delay/LMEs/LME_"$stat"_inny.nii.gz \
-resid /data/gcooper/movie_delay/LMEs/LME_"$stat"_inny_resids.nii.gz \
-model 'movie*moviepart+age+gender' \
-jobs 20 \
-ranEff '~1' \
-qVars "age" \
-qVarCenters "26.81" \
-num_glt 4 \
-SS_type 3 \
-gltLabel 1 'all' -gltCode 1 'moviepart : 0.333*beginning 0.333*middle 0.333*end' \
-gltLabel 2 'BvM' -gltCode 2 'moviepart : 1*beginning -1*middle' \
-gltLabel 3 'BvE' -gltCode 3 'moviepart : 1*beginning -1*end' \
-gltLabel 4 'MvE' -gltCode 4 'moviepart : 1*middle -1*end' \

The weirdness begins with glt4; 'all', which I'm using to calculate the mean effect of each level of the 'moviepart' factor. The main output of 'all' correctly contains some very large mean values (>120). All voxels containing a mean score greater than some mystery threshold are being assigned a z-score of zero in the subsequent 'all Z' brick.

I've since side-stepped the issue, as the z-score of these voxels can be correctly calculated 3dcalc -expr 'atanh(a)'

Is this a known issue? Is it an issue at all?



Edited 1 time(s). Last edit at 03/02/2023 10:46AM by gregetarian.
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Subject Author Posted

3dLME glitch(eye popping smiley?) - z-score outputs of post-hoc GLTs erroneously set to zero

gregetarian March 02, 2023 10:45AM

Re: 3dLME glitch(eye popping smiley?) - z-score outputs of post-hoc GLTs erroneously set to zero

gang March 02, 2023 01:03PM