How can I count the number of voxels above threshold in a functional dataset?
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Q36. 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 interfaces. See the output of 3dmaskave -help for the details.
What you are doing is creating a mask on-the-fly, by applying a threshold to a dataset sub-brick, rather than by drawing one manually with the Draw Dataset plugin. If the dataset were already thresholded externally (e.g., in 3dmerge), then you wouldn't have to use the Range controls, and just use the whole dataset itself as a mask for itself. Voxels that are zero in the mask sub-brick, either because they were zero ahead of time or were thresholded away using the Range controls, do not count in the calculation of the output.
A related problem is to count the number of voxels that meet two criteria; for example, the number of voxels in a FIM+ dataset with correlation coefficient greater than 0.4 and that have a Best Index value of 4. This can be done using 3dmaskave (but not the plugin) with a command like
3dmaskave -mask name+orig -mindex 3 -mrange 0.4 1.0 -dindex 1 -drange 4 4 name+origSub-brick #3 (Correlation) is thresholded, keeping only values between 0.4 and 1.0 (inclusive). Then sub-brick #1 (Best Index) voxels whose value is between 4 and 4 (inclusive) are counted up. (Program 3dinfo can be used to find out what sub-bricks are stored in a dataset.) The output of 3dmaskave will be something like
+++ 987 voxels survive the mask 4 [130 voxels]The first line says that 987 voxels were above the correlation threshold of 0.4 that was set with the -m* options to 3dmaskave. The second line says says that the average value of the selected voxels was 4 (not surprising here, since only allowed values of exactly 4 were counted), and that 130 voxels went into this average.
This FAQ applies to: Any version.
