Convert Scripts

1. Requirements

• pydicom
• nibabel
• pandas
• numpy

2. Converting .dcm to .nii.gz Files

• dcm2niix_HsinChu.py
  • This script has been abandoned.
• dcm2niix_Taipei.py

  • Do not use this script for decompression.

  • The dictionary should be like:

    /media/shard/data/ct_scan/raw/Taipei_2897/CGMH  <-- That is for argument `--data_root`
    ├── 0001  <-- here are the patient
    ├── 0003
    └── ......
    /media/shard/data/ct_scan/raw/Taipei_2897/ISP_annotation <-- That one should pass into `--isp_root`
    ├── 0001  # Almost like 502-CT
    ├── 0003
    └── ......
    

    • PS: To ignore parts that have already been processed, the --ignore_path should point to the --meta_dir.

  • The progress

    • A Skip ISP status indicates that the ISP folder does not contain any tissue labels.

3. Extract the centerline coordinates and names of each coronary artery and plaque.

python store_each_plq.py ...

4. To Merge Duplicate Plaque Labels

python combine_multi_plque.py ... 

5. To Match Text Report and CT

1. Choosing a Script Based on CT Imaging Source (Taipei or Hsinchu)
   • For Taipei: Specify the --meta_path argument. Its value should be the same as the --meta argument used in dcm2niix_Taipei.py.
     • Example:

       python text_match/maek_taipei_image_table.py \
         --meta_path <path/to/your/meta/data>
       

   • For Hsinchu: Specify the --hsinchu_root argument. Its value should be the same as the dst_root argument used in dcm2niix_Taipei.py.
     • Example:

       python text_match/make_hsinchu_image_table.py \
         --hsinchu_root <path/to/your/destination/root>
       

2. Merging Matched Image Cases and Reports To change the matching conditions, please modify the get_match_df method.

• Example:

  python text_match/merge_image_report.py \
   --image_table_path <Path to the output from make_taipei_image_table.py or make_hsinchu_image_table.py> \
   --report_label_path <Path to the desired report storage file> \
   --mode [taipei / hsinchu]
  

PS

• The dcm2niix program is available for download at dcm2niix
• Cardiac Structure ID to Name
  1. Right Atrium
  2. Right Ventricle
  3. Left Atrium
  4. Left Ventricle
  5. MyocardiumLV
  6. Aorta
  7. Coronaries8
  8. Fat
  9. Bypass
  10. Plaque