q02/rdmtools
11
0
Fork 0
Code Issues 3 Pull requests Projects Releases Packages Wiki Activity Actions
No description
36 commits 1 branch 0 tags 160 KiB
  • Python 100%
Find a file
Exact
Michał Szczepanik e46e3a1754 Add a script which updates the BIDS layout 
This is a scripted set of renames / deletions / file edits which change
an existing BIDS layout to a layout which uses acq-labels to distinguish
field maps and has correctly named dwi field maps (no dwi/...sbref).
This script also ensures one-to-one IntendedFor mapping between field
maps (field map pairs) and acquisitions if possible.

This should effectively obsolete `fix_dwi_sdc.py` & `peg_fieldmaps.py`,
because the same operations are done here.

The code will no-op when there is nothing to do, so it should be OK
to apply across subjects for whom the corrections above have already
been applied. Log messages are printed to provide an oveview of applied
changes.
2026-06-12 15:07:10 +02:00
trr379_rdmtools Add a script which updates the BIDS layout 2026-06-12 15:07:10 +02:00
.gitignore chore: ignore auto-generated version file 2026-03-19 09:45:00 +01:00
pyproject.toml feat: add ingest pipeline for JTrack data 2026-03-18 16:43:26 +01:00
README.md feat: ni_mannheim tooling 2026-01-16 19:28:15 +01:00

README.md

TRR379 RDM tools

Tools

These tools provide their functionality via several subcommands. They are fully documented in the tool itself. Run with --help, or <subcommand> --help to learn about the provided functionality.

bif_aachen

Utility for interacting with the TRR379 RDM system at the brain imaging facility (BIF) in Aachen.

This tool can be used without a dedicated installation step. Using uv, it can be executed directly from the TRR379 hub. To run the latest version, execute:

uv run https://hub.trr379.de/q02/rdmtools/raw/branch/main/trr379_rdmtools/bif_aachen.py

ni_mannheim

Utility for interacting with the TRR379 RDM system at the neuroimaging unit in Mannheim.

This tool can be used without a dedicated installation step. Using uv, it can be executed directly from the TRR379 hub. To run the latest version, execute:

uv run https://hub.trr379.de/q02/rdmtools/raw/branch/main/trr379_rdmtools/ni_mannheim.py

Recommendations

Some operations make frequent requests to the TRR379 hub. It is infeasible to run them without credential caching -- in particular with enabled two-factor authentication. It is therefore recommended to:

  • set up an access token at https://hub.trr379.de/user/settings/applications (with repository read/write permissions, including private repositories)

  • enable credential caching for a user account via running:

    git config --global credential.helper cache
git config --global credential.helper 'cache --timeout=3600'

    This configures credentials to be cached for maximum one hour.

Acknowledgements

This work was funded by Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant TRR379 (546006540, Q02 project)