Rtstruct Referencing Multiple CT Image Series

[DJ-CHB]

Hi,

Thank you for this tool, it really helped me with my work.

Currently I have a single rtstruct file which references to multiple 3D CT Images of different Series. I am using, rtstruct.get_roi_mask_by_name(roiname)

By removing the validation check, it works for me, but in most of the sequence I am getting a 3d mask -> 0s. Do you have any advice for me?

[asim-shrestha]

Hey @DJ-CHB

So i imagine you're using the load rt struct feature. The validations it does is firstly test the file is indeed an RT Struct and then subsequently test if all the counter data within the rt struct reference some file in the input dicom_series_path.

Given your rt struct references multiple series, what is your folder structure like and what are you passing in to dicom_series_path? I think you need to pass in the parent folder that contains all of the referenced series along with the ret struct.

Unfortunately, the code makes assumptions that the length of your input series will be the dimensionality of your 3D mask so this will lead to some further issues. (If each series has 30 layers and you have 3 referenced series, RTUtils will think that each roi should have 90 layers). Given this, you can separate out your RTStructs to only reference 1 series. Otherwise, we will need some code changes to allow for multiple series references

[DJ-CHB]

Hi @asim-shrestha

Thanks for your reply.

Yes, I am using the load rt struct feature. Well I have different folders for different ct series and I use the load rtstruct multiple times. It works for the base ct series, but gives mask3d.sum() as 0 for the rest of the ct series. I understand that I could keep all the files in one folder(I will try this out) and later separate it, but I have different shape for different series.