[Gate-users] HU Range Min/Max Incorrectly Rendered

Eric Nhu Nguyen ennguyen at stanford.edu
Fri Mar 4 19:41:25 CET 2022

Dear Gate Users,

I've come across the following issue when trying to run a simulation with CT images on a cluster using gjs job splitter:

As shown by the error message below, the HU range is not initialized properly, showing a [min,max] of [-1001,-1001] despite my patient-HU2mat.txt file actually covering [-1050,3001], which I double-checked.

[Core-0] Initialization of geometry

<!> *** WARNING *** <!> The image contains HU indices out of range of the HU range found in data/patient-HU2mat.txt

HU min, max: -1001, -1001

Image min, max: -1000, 1942

[Volume-0] ERROR: too many HU values are out of the range of the materials table:

******** 0 underflows (HU<-1001) ********

******** 249029 overflows (HU>-1001) ********

The warning only occurs in a minority of the split jobs, sometimes causing the job to end immediately, and sometimes after an hour or two of running just fine up to that point.

Strangely enough, the warning tends to disappear when the affected jobs are re-run. However, I would appreciate if anyone has any advice to prevent this from happening in the first place.

Thank you,


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