Brain mask used in ReHo calculation


I am concerned about the brain mask used in the ReHo calculation.  It includes voxels that are outside of the brain (like near the brain stem) and I wonder if the values that are within the brain mask but not within brain are included in the ReHo calculation near the brain edges.  In this case, these ReHo values near the brain edges will not be correct.  In addition, I cannot calculate an accurate mean or maximum ReHo value because values outside of the brain are included.  Is it possible to perform the ReHo calculation with a specified mask, like a gray matter mask?


Thank you for any insight and help on this matter,

Dina Dajani


Univ. of Miami

Use group mask generated in QC step will be better.



Which map are you referring to? the resampled GM? or whole brain?

Please look at the R-fRMI Course V2.0, Standardization section -> Generate group masks.



Hi Dr. Yan,

Hope this message finds you well. I have a few questions about creating a group mask with 2 runs per subject:

1) Does this module recognize the "S2" prefix and will it automatically average each subject's AutoMask files before generating the GroupMask?

2) If not, would it be appropriate to generate the GroupMask using all AutoMask files together (that is, all run1 AutoMask and all run2 AutoMask files)?

3) Otherwise, would it make sense to first create a new AutoMask for each subject by multiplying its two existing ones (using ImCalc)?

4) Finally, would it be sufficient to just use one of the two AutoMasks for each subject given that both runs should yield very similar AutoMasks? (If this is valid, it's definitely the simplest solution!)

Thanks in advance for your time,


1. No.

2. Yes.

3. You can do it.

4. I guess this is a valid point as you scanned them two runs in the same session.