bidscoin - Man Page

bidscoin [-h] [-l] [-p] [-i NAME [NAME ...]] [-u NAME [NAME ...]] [-d FOLDER] [-t [TEMPLATE]] [-b BIDSMAP] [-c Options [Options ...]] [-r] [--tracking {yes,no,show}] [-v]

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BIDScoin is a toolkit to convert raw data-sets according to the Brain Imaging Data Structure (BIDS)

The basic workflow is to run these two tools:

 $ bidsmapper sourcefolder bidsfolder     # This produces a study bidsmap and launches a GUI
 $ bidscoiner sourcefolder bidsfolder     # This converts your data to BIDS according to the study bidsmap

Default settings, plugins and template bidsmaps are stored in the `.bidscoin` configuration folder in your home directory (you can modify the configuration files to your needs with any plain text editor)

Set the environment variable `BIDSCOIN_DEBUG=TRUE` to run BIDScoin in a more verbose logging mode and `BIDSCOIN_CONFIGDIR=/writable/path/to/configdir` for using a different configuration (root) directory. Citation reports can be generated with the help of duecredit (https://github.com/duecredit/duecredit)

For more documentation see: https://bidscoin.readthedocs.io

-l,  --list

List all executables (i.e. the apps, bidsapps and utilities)

-p,  --plugins

List all installed plugins and template bidsmaps

-i NAME [NAME ...], --install NAME [NAME ...]

A list of template bidsmaps and/or bidscoin plugins to install

-u NAME [NAME ...], --uninstall NAME [NAME ...]

A list of template bidsmaps and/or bidscoin plugins to uninstall

-d FOLDER, --download FOLDER

Download tutorial MRI data to the DOWNLOAD folder

-t [TEMPLATE], --test [TEMPLATE]

Test the bidscoin installation and template bidsmap

-b BIDSMAP, --bidsmaptest BIDSMAP

Test the run-items and their bidsnames of all normal runs in the study bidsmap. Provide the bids-folder or the bidsmap filepath

-c OPTIONS [OPTIONS ...], --credits OPTIONS [OPTIONS ...]

Show duecredit citations for your BIDS repository. You can also add duecredit summary arguments (without dashes), e.g. `style {apa,harvard1}` or `format {text,bibtex}`.

-r,  --reset

Restore the settings, plugins and template bidsmaps in your home directory to their default values

--tracking {yes,no,show}

Show the usage tracking info {show}, or set usage tracking to {yes} or {no}

-v,  --version

Show the installed version and check for updates

examples:
 bidscoin -l
 bidscoin -d data/bidscoin
 bidscoin -t
 bidscoin -t my_template_bidsmap
 bidscoin -b my_study_bidsmap
 bidscoin -i data/my_template_bidsmap.yaml downloads/my_plugin.py
 bidscoin -c myproject/bids format bibtex
 bidscoin --tracking show

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