Hi Doug, It is finally starting to make sense to me. It was indeed the case that before Monte Carlo, within a cluster there were different values for each vertex, and after Monte Carlo, each vertex had the same value. I had difficulty understanding the different functions of the color scale min/max threshold and the vertexwise threshold. Is the following correct:
The min/max threshold is nothing more than a visualisation threshold; it does not change anything in subsequent analyses that are performed (such as Monte Carlo), it just decides which results are significant enough to be colored or opaque. The vertexwise threshold (the one that is next to Monte Carlo) is the one that decides which vertices should be considered in the simulation. So a vertexwise threshold of 2 only takes vertices into account that have a p value < 0.01. After Monte Carlo, the min/max (visualisation) threshold now decides which cluster wise p-values (cwp's) should be shown in color. So, compared to before Monte Carlo, it now has a slightly different function: it does not decide which individual vertices, but which clusters should be colored/opaque. One last question (if the above is correct): could one decide to set the vertex wise threshold at 1.3 for example, and the visualisation threshold at 2? Or do both threshold always have to be the same? Thanks a lot for your help, Anita _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
