Hello, I have second level analysis output from AFNI (2 sub-brick nifti files, 1 = mean, 2 = z-score) that I cannot figure out how to properly threshold in MRIcron. AFNI displays both positive and negative Fc in the same file so I am thinking this is where I am running into a problem? Attached is a screen shot where I import the overlay and the threshold is determined automatically. I also tried masking the data to the template to remove any confounding "zero voxels" outside the brain. Here is the output from 3dinfo for the file I opened: 

Number of values stored at each pixel = 2
-- At sub-brick #0 'SetA_mean' datum type is byte: 0 to 255 [internal]
[* 0.003159] 0 to 0.805545 [scaled]
-- At sub-brick #1 'SetA_Zscr' datum type is byte: 0 to 255 [internal]
[* 0.0509804] 0 to 13 [scaled]
statcode = fizt 

Any help/suggestions would be much appreciated.

Thanks,Sharyn

If you want to independently control the negative values and the positive values for a single overlay, you should just load the image twice. You can then set the positive and negative intensities independently. You can use the same principle for MRIcron or MRIcroGL. Since MRIcroGL allows full scripting, I prefer it for exposition. Here is the sample script you see if you choose the Scripting/Templates/Basic. Note it loads the same overlay "spmMotor" twice.
 1. For the first loading it hides values darker than +4, and clips values greater than +4 to +4, it also sets this layer to be 50% translucent.
 2. For the second loading, it hides values brighter than -4, and clips values darker than -4 to -4. It sets this overlay to have the blue color scheme: