Now You can download and convert Your data on any machine using xnat_dcm2bids package.

Quickstar Notebook

How to bids on Calcus vel How to BIDS in 2024

Quick sheet

<aside> 💡 Log in to Calcus (Terminal): ssh [email protected]

</aside>

<aside> 💡 DICOM files should be placed in ./sourcedata directory within Your project

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<aside> 💡 Activate (install) dcm2bids source neurodesk/bin/activate

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<aside> 💡 Run conversion script tail -n +2 ../kj23a.csv | parallel -j 4 --colsep ',' ../run_dcm2bids.sh "{1}" {4} {5}

</aside>

Create Your Project’s directory

Go to /home/repo

Activate (install) dcm2bids source neurodesk/bin/activate

Create an empty structure of directories dcm2bids_scaffold -o project

Go to Your project’s directory cd project

Put or create a link to config.json in project/code/ directory.

Get DICOM data

Your DICOM files are always available through xnat.nencki.edu.pl from any computer, but Calcus has a better, direct connection. Please make sure the ./sourcedata directory is available within Your project. It should be synced with XNAT every night. Let me know if something is missing.

Prepare Your CSV dictionary

Export XNAT sessions to CSV

Put the CSV in project’s directory. You can’t upload the file to /home/repo using SMB (Finder) but You can move it in Terminal withcp ~/new.csv /home/repo/project/