Mask for 3dSetupGroupInCorr

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Dear AFNI experts,

I pre-processed using afni_proc.py (example #11a) resting state data. I have two groups of participants (teenagers and adults). I am now looking into using the program 3dSetupGroupInCorr to set up the data to run 3dGroupInCorr.

In the documentation, it is mentioned that all datasets use the same mask. To be clear, I need to create a group mask that encompasses both teenagers and adults. Is this correct? In other words, I would create a group mask with all participants included and then run 3dSetupGroupInCorr for each group with that mask. Is this correct?

Also, in the documentation, in the example given, the mask is created from individual EPI automasks by using 3dMean and 3dcalc. Looking at the output of my afni_proc.py script, I have 3 types of mask:

  1. mask_anat_S203_FS+tlrc
  2. mask_group+tlrc
  3. mask_epi_extents+tlrc

From reading documentation online, I saw that the mask_group+tlrc can be used to create a group mask using 3dMean. Could I use this anatomical mask instead of an EPI mask to input into 3dSetupGroupInCorr? If not, where do I find the EPI mask at the subject level in the output directory?

Thank you very much,

Isabelle

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Hi Isabelle,

This should be the same make you use for multiple comparison
correction. So yes, it should apply to both sets of subjects.

A common way to make an EPI mask is from the full_mask
datasets. Consider example c2 from “3dmask_tool -help”.

  • rick