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Dr. Mike

Fiji changing voxel values?

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I've noticed that Fiji alters voxel values when an imported TIFF stack is saved as NRRD file format. Voxels are about 32,000 higher than they should be. This causes problems when running the NRRD file through the democratiz3D conversion service. as the values are well outside the normal range. Does anybody have experience with Fiji and have a solution to this problem?

 

Thanks in advance.

 

Dr. Mike

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I haven't worked with a tiff stack but I wonder where it gets the voxel size values from?  I would check the tiff meta data and see what values are there.  Guessing images are in DPI and fiji reads the values as mm... but then I would think the voxel size would be much smaller.  I would expect the same result from ImageJ but worth a try too.

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The problem isn't the voxel size, but rather the voxel value. In other words, a value that is 10 hounsfield units (water) becomes 32000 or so in fiji. I'm thinking that the voxel values are as a signed integer but fiji reads it as an unsigned one. Not sure but anytime I use fiji I seem to run into this problem.

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