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Greeting to all the awesome fellow SPMers who are reading this post! Do I have a question for you at this perfect time of day (i.e answers from all time zones are accepted)!  Stan is an equal opportunity listener :)

Now let’s get to business. As I understand, SPM has the masking threshold set to 0.8. Areas that are susceptible to B0 inhomogeneities experience rapid dephasing following an RF pulse, which leads to dropouts of the areas I tend to study (namely MTL and OFC). SPM then computes the global signal and if a given voxel is less than 0.8 of that value, SPM treats that voxel’s signal as NaN during the regression. Correct?

So here’s the question. Is it OK to lower this value to retain more of the low signal data and what are the consequences of doing so? After all, Karl's group set this value to 0.8 for a reason. Does the SNR of BOLD become exponentially worse once the data falls below this cutoff?

To retain some areas that are prone to dropouts in the group analysis, one approach is to proceed with the masking threshold set at 0.8, but to use GLMflex to keep voxels that are present in at least n subjects during the group model. Is there any standard for the percentage of data points that should be kept for the second level analysis in GLMflex? Currently, my analysis is set up in such a way that a given voxel must be present in at least 60 percent of the subjects to be considered for the group GLM. I am all ears for ideas on how to optimize these parameters.

And last, but not least. It should theoretically be possible to force SPM to keep all the voxels in the subject-level analysis and to forego GLMflex, sticking instead with SPM’s group-level procedure. What are advantage/disadvantages to this approach? And how would it compared with GLMFlex. I am particularly interested in hearing from folks who tried to compare this approaches in a quantitative manner. 


Well, we’ve come to the end of this (hopefully not too boring) wall of text :) … To all those who leave a constructive answer, I am giving away virtual hugs for free!  :-)   …. And if you happen to live in Edmonton (AB, Canada), I will even buy you a pint of Guinness at Sherlock!

Many thanks,

Stan