Agent 007-

We did a build yesterday, and the newest code has updates+fixes based on your comments---thanks very much for noticing those things.

Firstly, the Mean table values by default will *not* be absolute valued; if anyone wants that, they can use this new option:

-abs_table_data :(new, from Apr 29, 2021) Use the absolute value of voxel
                 intensities (not the raw values) for calculation of the
                 mean and Standard Error of the Mean (SEM) in the report
                 table. Prior to the cited date, this was default behavior
                 (with '-noabs' switching out of it) but no longer.

Secondly, the scale factors will be applied, too. (I'm not sure when they got ignored in the code, but that is fixed now.)

For what to do with the ROI values in modeling, that might be better to ask as a separate thread. 3dLMEr is probably a good start, but exactly which way to go and how to model depends on what other data you have, what your study design is, etc. Perhaps you have also seen Gang's note on 3dLMEr.
[afni.nimh.nih.gov]

For some more takes of region-based analysis, this is also some of Gang's newer work (describes the program RBA for region-based analysis):
Chen G, Xiao Y, Taylor PA, Rajendra JK, Riggins T, Geng F, Redcay E, Cox RW (2019). Handling Multiplicity in Neuroimaging Through Bayesian Lenses with Multilevel Modeling. Neuroinformatics. 17(4):515-545. doi:10.1007/s12021-018-9409-6
[pubmed.ncbi.nlm.nih.gov]

--pt