I have created a tractogragram of 50 million streamlines based on an ROI seed, and I then ran tckmap to super-resolve the data at 500 microns. The output is very nice, but there are some regions where there are bright hotspots (see the picture below). I have carried out various mrcalc commands on the .mif output (e.g. log, log10, sqrt) in an attempt to make the intensities more linear, but the bright spots still appear. I have played with the various threshold and intensity settings but to no avail.
Could you please offer some advice on how to address this? Also, could you please clarify the differences between the ‘colour map and scalings’, thresholds, and the scales under View Options (in rendered mode) i.e intensity scaling, transparency, thresholds, and alpha?