Automated PyRadiomics Feature work with DICOM(input image volume) and DICOM RT structure (input regions)

[youngchanseo (서영찬 / 학생 / 의료기기산업학과 ­)]

Hello.

I have already installed pyradiomics and Slicer RT via extension manager.

In the DICOM RT structure file, there are contour data for regions of interest (ROIs) [1]) of the tumor shape.
In the DICOM file, I have an MRI of the patient.
I searched for Radiomics in the 3d slicer’s module and ran it. I put the DICOM RT file in the “input regions” and the MR image in the “Input Image Volume”.
As shown in the image below, I was able to successfully extract the Radiomics Features from the MR image of the ROI (Tumor).

Here I have two questions

1. the features and calculated values are displayed in a table, but is it possible to export them to an excel file?
   

   

2. i need to do these operations multiple times. So I want to do these labor intensive things automatically.
   Is it possible to automate this with python code?
   For example, I have 100 RT structure (outlined tumor regions) DICOM files and 100 DICOM (MR brain) images, can I use code to automatically extract features in pyRadiomics & 3d slicer to do the work at once?
   

   

[1] Create and Display 3-D Mask of DICOM-RT Contour Data - MATLAB & Simulink - MathWorks 한국

[cpinter (Csaba Pinter)]

1. Click on the save button, only select the table node, then choose either csv or tsv, and save. You can open it in Excel
2. Yes. I suggest starting from the script repository and look at the code of Slicer and the extension itself when in doubt. The forum contains a lot of topics about python automation of certain workflows as well.