bidscoiner - Man Page

bidscoiner [-h] [-p LABEL [LABEL ...]] [-b NAME] [-f] [-c [SPECS]] sourcefolder bidsfolder

Converts ("coins") your source datasets to NIfTI/json/tsv BIDS datasets using the mapping information from the bidsmap.yaml file. Edit this bidsmap to your needs using the bidseditor tool before running bidscoiner or (re-)run the bidsmapper whenever you encounter unexpected data. You can run bidscoiner after all data has been collected, or run/re-run it whenever new data has been added to your source folder (presuming the scan protocol has not changed). Also, if you delete a subject/session folder from the bidsfolder, it will simply be re-created from the sourcefolder the next time you run the bidscoiner.

The bidscoiner uses plugins, as stored in the bidsmap['Options'], to do the actual work

Provenance information, warnings and error messages are stored in the bidsfolder/code/bidscoin/bidscoiner.log file.

sourcefolder

The study root folder containing the raw source data

bidsfolder

The destination/output folder with the bids data

-p LABEL [LABEL ...], --participant LABEL [LABEL ...]

Space separated list of selected sub-# names/folders to be processed (the sub-prefix can be omitted). Otherwise all subjects in the sourcefolder will be processed

-b NAME, --bidsmap NAME

The study bidsmap file with the mapping heuristics. If the bidsmap filename is just the base name (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml

-f,  --force

Process all subjects, regardless of existing subject folders in the bidsfolder. Otherwise these subject folders will be skipped

-c [SPECS], --cluster [SPECS]

Use the DRMAA library to submit the bidscoiner jobs to a high-performance compute (HPC) cluster. You can add an opaque DRMAA argument with native specifications for your HPC resource manager (NB: Use quotes and include at least one space character to prevent premature parsing -- see examples)

examples:
 bidscoiner myproject/raw myproject/bids
 bidscoiner -f myproject/raw myproject/bids -p sub-009 sub-030
 bidscoiner -f myproject/raw myproject/bids -c "--time=00:30:00 --mem=4000"

Marcel Zwiers <m.zwiers@donders.ru.nl>