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

[G Tom]

If it helps anyone these are the commands I use:
# Create a mask of the  BODY/EXTERNALcontour
clitkDicomRTStruct2Image -i ../RS.Test_Dicom_MC.Str1.dcm -o
patient-mask.mhd -n BODY -j patient.mhd

# Set outside BODY/EXTERNAL to air"
clitkSetBackground -i patient.mhd -m patient-mask.mhd -p -1000 -o
patient-cleaned.mhd

Thank you

GT

On Thu, Mar 18, 2021 at 12:27 AM G Tom <gregthom992 at gmail.com> wrote:

> 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
>
> [image: image.png]
>
>
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