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Miscellaneous Tools

Justin Wang edited this page May 12, 2022 · 12 revisions

Information about miscellaneous tools of the pipeline.

Reparcellation Tool

The TVB-UKBB pipeline generates multiple parcellation-specific outputs during the regular processing of a dataset. Users may choose to process the same subject with multiple different parcellations.

Instead of re-running the entire pipeline and needlessly repeating non-parcellation specific processing, the reparcellation pipeline only executes parcellation-specific portions of the regular pipeline.

Reparcellation tool details can be found here.



QC Report tar Tool

The QC Report can be extracted from a processed subject and compressed into an archive named sub-XXXXX_QC.tar. The QC report included in the tar is standalone and portable. No software is required to view the report, only a browser. The tar sits at ~100MB for each subject. This allows users to view QC Reports on any computer and eliminates the need for X forwarding over SSH to perform quality control.

The QC tar is not generated by the pipeline and requires users to run:

bb_pipeline_tools/QC_tar.sh sub-XXXXX

A batch option exists with:

bb_pipeline_tools/QC_tar_batchcopy.sh subject_list.tsv

subject_list.tsv is a file with a list of subject IDs, one per line. This will generate the QC tars in a directory called QC_tar.



BIDS Conversion Tool

The TVB-UKBB pipeline outputs can be reorganized and renamed to follow the Brain Imaging Data Structure (BIDS) standard. The tool can be found here. If you edit the pipeline such that it generates new derivative data in a non-BIDS format, you will need to edit the dictionary to include the newly generated files and their desired BIDS-compliant filenames and locations. Usage instructions for running the BIDS tool here.

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