README.md

MRT Extraction from PACS Archiv Server and Labeling with Biopsie Data

Autor: Marius Schmitz

Content:

This Reposotory contains Python Scripts to find Patients in the PACS System and to extract Images from a PACS Archive Server. It also provides Scripts to generate Label, for RESIST Markers and a Script to create a Summary of Meta Data information in an Excel Tabel.

generate.py

Image Extraction

Input (change Paths inside Code):

1. .txt File with IP and Port of the PACS Server
2. .csv File with patient Ids
3. output directory

Output:

A Directory with subdierctories for each Patient

Note:

You can filter the images before extraction with modifications inside the 'copyImagesForPatient' Methode.

generateStudySummary.py

Generates Metadata summary

Input (change Paths inside Code):

1. Folder structure like the output of 'generate.py'
2. output directory

Output:

A Excel File with columns for each Series of all Patients

Note:

Change used Tags in the 'series_meta_tags' list

labelDataset.py

A tool to label a Series of MRT images with RESIST markers

Input (change Paths inside Code):

1. Folder with only .dcm files
2. output directory
3. A Patient Id as Param when calling the script
4. File with Biopsie Data

Output:

.txt files with markers

Note:

The Biopsie Data is shown in the Tool and can help while labeling the images. To Navigate inside the tool use keys listed inside 'on_press' methode.