CVC-Coating: Catheter-related thrombosis in central venous catheter coated with/without chlorhexidine

We use guix to ensure an reproducible computing environment.

Bootstrap

Guix on debian

sudo apt install make git git-annex guix

Fetch sources

git clone git@github.com:umg-minai/crt-chx.git

Build manuscript

Running make the first time will take some time because guix hast to download the given state and build the image.

make

Modify the manuscript

All the work has to be done in the sections/*.Rmd files.

Make targets

• make shell create reproducible environment (guix shell with specific parameters).
• make clean removes all generated files.

Initial setup

Init git-annex

https://git-annex.branchable.com/

WEBDAV_USERNAME=xxx WEBDAV_PASSWORD=xxx git annex initremote uni-greifswald-nextcloud type=webdav url=https://nextcloud.uni-greifswald.de/remote.php/dav/files/gibbs/9726.crt-chx/git-annex chunk=10mb encryption=none

git annex initremote ant type=rsync rsyncurl=antl:/media/wd/cvc-coating/git-annex chunk=10mb encryption=none

Install DICOM viewer

https://weasis.org

wget https://github.com/nroduit/Weasis/releases/download/v4.6.6/weasis_4.6.6-1_amd64.deb
sudo dpkg -i weasis_4.6.6-1_amd64.deb

Usage

Update DICOMDIR files

Fix different named IDs and update DICOMDIR file.

make rewrite-dicom-ids

Troubleshooting

Sometimes duplicated SOPInstanceUIDs appear:

W: file GEMS_IMG/2025_OCT/18/__19116/PAIJ2DG6: directory record for this SOP instance already exists

Find duplicated files:

bin/dcmdup.sh GEMS_IMG/2025_OCT/18/__19116/PAIJ2DG6

Compare the duplicated files:

bin/dcmdiff.sh GEMS_IMG/2025_OCT/18/JD190116/PAIJ2BO2 GEMS_IMG/2025_OCT/18/__19116/PAIJ2DG6

Overwrite study ID:

guix time-machine --channels=guix/channels.pinned.scm -- shell --manifest=guix/manifest-dcm.scm -- dcmodify --insert "(0020,0010)=MG07-00" --no-backup GEMS_IMG/2026_FEB/24/JD202502/Q2OKF082

List non-study DICOM files:

make list-non-study-dicom

Use git annex

git annex add largefiles
git commit -m "what was done"
git annex sync --content # to publish the files on the remotes

Predecessor study

https://umg-minai.github.io/crt/

Contact/Contribution

You are welcome to:

• submit suggestions and bug-reports at: https://github.com/umg-minai/cvc-coating/issues
• send a pull request on: https://github.com/umg-minai/cvc-coating/
• compose an e-mail to: mail@sebastiangibb.de

We try to follow:

• Conventional Commits
• Semantic Line Breaks