[Brains-users] Problems thresholding dark images

[Kevin Berne]

Hello again,
Thank you for your insightful guide and for the time it took you to write it. I have applied it to my images and found it working up to a certain point, but not beyond. To be more specific, I loaded the unresampled T1, applied my transform to it and also loaded the talairach.bnd and .box. Converting the box to a mask and measuring the image mask also worked without any problems, resulting in a maximum intensity of about 29 (assuming I picked the right value out of the many, it was fittingly named "maximum""). Adding the 20 you mentioned to it would therefore bring us up to 49.
With the removal of bright stuff from the image the trouble basically starts. After thresholding the image with 0, resulting in a uniform whole-image mask and entering the requested line "b2 clip image i1 m2 upper-bound= $threshold" replacing $threshold with the value 49 into the Advance Console, which our Brains2 does in fact contain, just another uniform mask is created. Adding up the clipped images only results in more uniform patterns. There seems no recognizable image to be found after the application of the process, for whatever reason. Measuring the resulting image displays minimum and maximum values both as 49, 98 after adding it too itself. 
If you would happen to know how this can be resolved, I would again be very grateful, as always.
In the meantime, a nice weekend to everyone!

Kevin Berne
ZI Mannheim
Central Institute of Mental Health
J 5
D-68159 Mannheim
Germany

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