[Gate-users] use dicom ct in simulations: override HU outside BODY/External Contour to air

[G Tom]

Hi,

I am trying to use a ct dataset for my simulations. I use vv to convert
dicom slices to mhd like so

clitkDicom2Image -o test.mhd *.dcm

This is fine and I get the mhd/raw files but I have the associated
structures with a BODY/EXTERNAL contour and want to crop/mask the ct so
that all voxels outside of the External/ BODY contour are set to HU of AIR.

Does anyone have a straightforward way to do it ?

First I tried creating a mask of the body structure but the result is not
satisfactory; vv seems to only binarize every other slice. I used the
command:

clitkDicomRTStruct2Image -i RS.Test_Dicom_MC.Str1.dcm -j
ct/'CT.Test_Dicom_MC.Image 1.dcm' -c -n BODY -o bodymask.mhd

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