Hi, Taylor,

Thank you very very much - I have read it very carefully. Very informative and professional. Two further questions:

Quote
---> this one says take the part of the input dset and make a mask wherever it has a value >3, and multiply that mask region by the actual value there (output type: short):
3dcalc -a TT_N27_grey_seg.nii.gz -prefix TT_N27_grey_seg_short -datum short -expr 'a*step(3-a)'
---> while this one says: return a copy of the input dset as dtype=short (the "-expr a" works no math on the input).
3dcalc -a TT_N27_grey_seg.nii.gz -prefix TT_N27_grey_seg_short -datum short -expr a
I don't see why it would be necessary to convert to short, but OK?
--> and this command would resample the input dset to Reward* grid, sure:

So my understanding is that this step is not necessary. If people want to do it, then the 2nd command (I copy it below) is better, as it does not set anything there, right?
3dcalc -a TT_N27_grey_seg.nii.gz -prefix TT_N27_grey_seg_short -datum short -expr a

Quote
Re. your question here:
Quote
I am also confused why here the template need be the output from the group analysis (i.e, Reward_vs_Neutral_ShapeNonfixed+tlrc). It looks like a circular argument, as we want to get a mask for the next group analysis (e.g., 3dttest++ and/or ANOVA2). But here the template is from the group analysis output. Something must be wrong. Any good pointers?
... I don't quite understand. The "template" in 3dfractionize just provides the grid for resampling your GM mask (assuming it is on a different grid to start with? if it weren't you wouldn't need to fractionize it). I don't understand what the issue is, or what circularity you are referring to?

I understand more about the 3dfractionize usage from here. What I said circularity here means

3dfractionize -template ./Reward_vs_Neutral_ShapeNonfixed+tlrc. -clip 0.2 -preserve -prefix TT_N27_grey_seg_short_F -input TT_N27_grey_seg_short+tlrc.

1) For the command above, the aim is to generate a mask for the Group analysis, and with this mask (i.e., TT_N27_grey_seg_short_F), people will get group analysis outputs, including the one, "Reward_vs_Neutral_ShapeNonfixed+tlrc."

2) But now before they run the group analysis, they use the "Reward_vs_Neutral_ShapeNonfixed+tlrc." as the 3dfractionize template, to make a mask (which finally is for the group analysis). Before people do the group analysis, they should NOT have this input "Reward_vs_Neutral_ShapeNonfixed+tlrc.".

3) Since people should NOT have the "Reward_vs_Neutral_ShapeNonfixed+tlrc." during the 3dfractionize stage, what should be the input template for this command?

Thank you very very much,
J