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CSI 8 Conversion

Michael Satterfield
Updated

ONLY FOR INTERNAL REFERENCE BY CONVERSION TECHNICIANS, DO NOT PROVIDE OUTSIDE THE ORGANIZATION

We do not officially support converting from CSI version 8. 

There are a few issues that prevent the converter from finding and converting the images.   We do have partial workarounds for these issues, but they have to be done manually by the conversion technician.

ISSUES & WORKAROUNDS

Issue 1:  Image files all have .DCM extension. Converter is only looking for images with their traditional extensions:  .RVG, .PANO, .CEPH, .STV, .SC, .CRIO, .CRPANO, .TIF

Fix:  Duplicate the entire  CSI image folder

  1. Create a new directory D:\CSI8-COPY    (or use drive letter with the most free space)

  2. Go to the  \PWImages\Patient or \TW folder

  3. Put the following two files in this Patient or TW folder.

  1. Open a command prompt from this folder

  2. From the PWImages\Patient or \TW folder, run: 

xcopy .\*.dcm D:\CSI8-COPY  /s /exclude:exclude.txt   > xcopy-log.txt

(replace D:\CSI8-COPY with the destination for the copy)

(make sure your exclude.txt is saved in the PWImages\Patient or \TW folder)

  1. Duplicate FMS files as well (excluding F1.fms, F2.fms, etc): 

    1. Open a command prompt from the same folder.

    2. From the PWImages\Patient or \TW folder, run: 

xcopy .\*.fms D:\CSI8-COPY  /s /exclude:exclude-FMS.txt   > xcopy-log-FMS.txt

(replace D:\CSI8-COPY with the destination for the copy)

(make sure your exclude-FMS.txt is saved in the PWImages\Patient or \TW folder)

Then rename all the .DCM extensions back to .SC, .PANO, .RVG, .STV (based on approx file size and modalities, not always accurate)

Fix 1:  SCRIPT TO RENAME EXTENSIONS:   dcm-file-rename.exe

This script will attempt to rename all .dcm file extensions based on the DICOM modality (PX = .pano, IO = .rvg, XC = .stv, all other modalities = .rvg)

  1. Place this EXE in the CSI8-COPY directory.

  2. Open command prompt from CSI8-COPY directory.

  3. Run dcm-file-rename.exe

  4. When asked, specify the path to the CSI8-COPY folder, for example:  D:\CSI8-COPY\

  5. The script will log the results to a file: dicom_processing.log. Review the log for errors or issues with renaming.

Fix 2:  (ONLY DO IF FIX 1 FAILS) Manually rename files:

  1. Search the CSI8-COPY folder for *.dcm and sort by size smallest to largest

  2. Look at the file size ranges and check several images in the range by opening them in DicomViewer, to get an idea of which files should be assigned which modality (.rvg for  IO, .pano for PX or OT, etc).

  3. Select a range of files to be renamed.

  4. Shift+right-click and click Copy as Path

  5. Open Notepad++ and paste

  6. Search and replace:

    1. Find: ^

    2. Replace: ren<SPACE>       (note, replace <SPACE> with a space character)

    3. Find: \\([^\\]+)\.dcm"

    4. Replace: \\$1\.dcm" "$1\.rvg"      (note: replace rvg  with the new extension you want to assign to that range of images, for example: rvg, pano, sc, stv)

  7. Save the Notepad++ document as a .bat file.

  8. Open a cmd prompt as administrator. Navigate to the .bat file location.

  9. Run the .bat script

  10. Repeat steps 3-8 for other file types to change their extensions

Issue 2:  All the CSI layout definition files (.FMS) are expecting  image files with ".dcm" extensions. Without these templates, the images would all be converted as single images, and missing some image filtering.

Fix 1: Only use if Fix 1 above succeeded. Script to update all FMS files in the CSI8-COPY directory with the new .dcm file extension:

This script will scan for FMS files, find any .dcm entries in the files, and update the file extension with the new current extension (.rvg, .pano, .stv).

  1. Copy this script to the CSI8-COPY directory

  2. Open a command prompt from the CSI8-COPY directory

  3. Run the fms-file-update.exe

  4. When prompted, specified the CSI8-COPY folder, for example:  D:\CSI8-COPY

Fix 2:  (Only use if Fix 2 was used above. Skip this step if Fix 1 above succeeded) Batch replace all ".dcm" in every FMS file with ".rvg" (or the extension that was used)

RUN NOTEPAD++ AS ADMINISTRATOR

Then go to Search > Find in Files:

image-20250416-182024.png

THEN CONVERT DIRECTLY TO DICOM, NOT TO XV FIRST

ALTERNATIVE:  Push DCM files directly to Apteryx:

Open Command Line and use 

dir /b /s *.dcm

and then get a list of only the DCM files to copy to the Apteryx-images folder.

PROBLEM WITH THIS OPTION:  PANS and 16-BIT images are getting scrambled during upload. The converter handles these properly.

Another issue:  Duplicate patient records are created - some patients missing birthdate and gender, some with nickname field filled in, others with extra comma in name.

Fix:  Data mapping needed to merge duplicates

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