[Brains-users] Still problems thresholding images...

[Kevin Berne]

Hello,
Sadly I have to report that still, whether I try and convert the images to 16bit or not at whatever stage, after manually thresholding the image to 0 and the appearance of the uniform mask no image can be created by using the line "b2 clip image i1 m2 upper-bound= $threshold", in consequence only more uniform masks appear. However, the 16bit versions seem to contain a larger dynamic range, namely about max180 when measuring the brain.box mask. Nonetheless, before and after adding the processed images up only uniform masks appear (after destroying all the other masks or un-displaying them through using the selector button). So, nothing seems to have changed.
I have attached a zipped image set. This represents what I have been working with until now, at least the T1 part of it. Normally, I pre-process the images using MRIcro, because I used to have problems opening our images with my last version of Brains2 and still have with interleaving the T2 part, which also seems to be quite tricky. Therefore, at this moment I give the images a pre-Brains2 workup using MRIcro to avoid those difficulties. Since Brains2 now seems to open the raw files too, I have given them a try with the recommended and described procedure (saving as 16bit, thresholding...), sadly with the same flawed aforementioned results.
So the attached files do not represent raw images, but ones treated with MRIcro and resampled (8bit, as far as I can tell) including image math adding using Brains2. Since I can only send small files up to 4MB at this point, I could not give you more, but since this represents the kind of files I have to work with right now, it would be nice if you could give it a try to see if you can process them.
If you find any irregularities with them and have more recommendations or tips, I would be glad to hear them.
Thank you very much for your patience,
Kevin Berne

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