I am using MRIcroGL 1.2.20190902 Cocoa on Mac OS Sierra 10.12.6

On prior versions, under File/Add Overlay, there was an option to remove small clusters which no longer appears.

Is this option going to return? I need to remove small clusters to match my extent thresholded figures in SPM.

Thanks,

Jake

I have submitted an enhancement request for you. Feel free to submit any others you have. While this is not hard, I have a lot of other things on my plate, so don't expect a fast response. The project is open source, so you can make a fork and add features - once you are happy with them you can issue a pull request to share your solution.

Since you note you are using SPM, this suggests you have Matlab. Therefore, you can use my Matlab script to create a cluster threshold.

Originally posted by Chris Rorden:
Thanks, I will give this a shot, using SPM to save all clusters (n-ary) style the Display/Save in the lower Results window seems to work as well.

Assuming your statistical map is lower resolution than the background image, I would strongly encourage you to threshold the data AFTER it has been upsampled, rather than BEFORE. Due to spatial smoothing, the non-significant neighbors of significant voxels are very likely to be ALMOST significant. However, this information is lost when you threshold the data. If you plan to upsample data that has been already thresholded, I would male sure you have "Load Smooth Overlays" unchecked in the "Options" pulldown of the "Layers" panel. The overlays may appear jagged if you do not smooth them, but smoothing data that has been masked can be misleading. You want the interpolation to work with all the available data.

I mention this briefly in the cluster threshold scripting page.

Originally posted by Chris Rorden: Good point, I had not considered this.