I$\text{'}$m working on a survival analysis project using CT scans with a CNN model. After loading DICOM files for one patient and converting to Hounsfield Units $($HU$),$ I get a $134$x$512$x$512$ array. Resampling changes this to $402$x$500$x$500.$ However, slice counts vary between patients. I have corresponding mask images for each patient's CT scan.

Given this scenario, I need guidance on the following:

Post$-$HU Conversion and Resampling Steps: a$)$ What specific steps should I take after converting to HU and potentially resampling? b$)$ Is there a need for further normalization or scaling of the HU values? c$)$ How should I handle windowing of the CT images, if necessary?

Mask Integration: a$)$ What's the best way to incorporate mask data with the processed CT images? b$)$ Should masks be processed differently from the main CT data?

Handling Variable Slice Counts: a$)$ What methods are most appropriate for standardizing inputs with different slice counts in survival analysis? b$)$ How might this affect the model's ability to analyze survival data?

Exact CNN Model Input for Survival Analysis: a$)$ What should be the precise shape and format of the input tensor for a CNN model in survival analysis? b$)$ How many channels should the input have, considering both CT and mask data? c$)$ What data type and value range is optimal for the input tensors?

Survival Data Integration: a$)$ How should survival data be incorporated with the imaging data for input into the CNN$?$ b$)$ Should it be part of the input tensor or handled separately in the model architecture?

Final Preprocessing Pipeline: a$)$ Can you outline a step$-$by$-$step preprocessing pipeline from raw DICOM to final model input? b$)$ What quality checks should be implemented at each stage?

Please provide a detailed guide addressing these points, with a focus on the exact steps after HU conversion and resampling, and the precise input format for a CNN model in survival analysis. Include any relevant Python code snippets, particularly for critical steps in preparing the final input tensor. Your guidance should help ensure that the preprocessing maintains the integrity of the medical images while optimizing them for survival analysis in a CNN model.