How can I count the number of voxels above threshold in a functional dataset?
There are 2 slightly clumsy ways to do this counting, one from the command line and one from a plugin. They are basically the same. From a plugin: use the ROI Average plugin. Choose the Source and Mask datasets to be the same. Choose the sub-bricks to be the same, and to be the one you want to threshold on (e.g., for fico datasets, the correlation coeffient is in sub-brick #1 — in general, you can use the Define Datamode->Misc->Func Info item to get information about a dataset’s sub-bricks). Use the Range control in the plugin to set the range of values from the sub-brick you want to include (e.g., for fico datasets, you might set the range to be 0.5 to 1.0 to include all voxels with correlation coefficient between these values). Then press Run+Keep and you’ll get a popup window with the summary information you want. The same thing can be done using the 3dmaskave command line program – which isn’t surprising, since the plugin and the program are almost identical, except for their inte
