bidsgnostic

BIDS app to view:

• the dataset content
• events file content

Install from github with pip

pip install -e git+https://github.com/Remi-Gau/bidsgnostic#egg=bidsgnostic

Note: you can re-run this command to re-install with the latest version

Usage

short form

participant level

bidsgnostic /path/to/bids/dir /path/to/output/dir participant --cores all

See here for participant level interactive figure as html.

Figures will not be generated if your events have more than 14 type of events. If that is the case use the include argument to select which events you want to see.

group level

bidsgnostic_layout /path/to/bids/dir /path/to/output/dir group

See here for group level interactive figure as html.

all the gory details of the API

subject Level

usage: bidsgnostic [-h]
                [--pybidsdb-dir PYBIDSDB_DIR]
                [--reset-db]
                [--force-output]
                [--help-snakemake]
                [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                [--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...]]
                [--derivatives DERIVATIVES [DERIVATIVES ...]]
                [--log_level LOG_LEVEL]
                [--filter-events FILTER_EVENTS [FILTER_EVENTS ...]]
                [--wildcards-events WILDCARDS_EVENTS [WILDCARDS_EVENTS ...]]
                [--path-events PATH_EVENTS]
                bids_dir output_dir {participant}

Snakebids helps build BIDS Apps with Snakemake

optional arguments:
-h, --help              show this help message and exit

STANDARD:
Standard options for all snakebids apps

--pybidsdb-dir PYBIDSDB_DIR,
                        Optional path to directory of SQLite databasefile for PyBIDS.
                        If directory is passed and folder exists, indexing is skipped.
                        If reset_db is called, indexing will persist
--reset-db,
                        Reindex existing PyBIDS SQLite database
--force-output,
                        Force output in a new directory that already has contents
--help-snakemake,
                        Options to Snakemake can also be passed directly at the command-line,
                        use this to print Snakemake usage

SNAKEBIDS:
Options for snakebids app

bids_dir                The directory with the input dataset formatted according to the BIDS standard.

output_dir              The directory where the output files should be stored.
                        If you are running group level analysis this folder should be prepopulated
                        with the results of the participant level analysis.

{participant}           Level of the analysis that will be performed.

--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...],
                        The label(s) of the participant(s) that should be analyzed.
                        The label corresponds to sub-<participant_label>
                        from the BIDS spec (so it does not include "sub-").
                        If this parameter is not provided all subjects should be analyzed.
                        Multiple participants can be specified with a space separated list.

--exclude_participant_label EXCLUDE_PARTICIPANT_LABEL [EXCLUDE_PARTICIPANT_LABEL ...],
                        The label(s) of the participant(s) that should be excluded.
                        The label corresponds to sub-<participant_label> from the BIDS spec
                        (so it does not include "sub-").
                        If this parameter is not provided all subjects should be analyzed.
                        Multiple participants can be specified with a space separated list.
--derivatives DERIVATIVES [DERIVATIVES ...]
                        Path(s) to a derivatives dataset, for folder(s)
                        that contains multiple derivatives datasets (default: False)
--log_level LOG_LEVEL,
                        The log_level level of the reporting
                        that will be printed to the console.
                        The default is "0", which means that
                        only warnings and errors will be reported.
                        If set to "1", all warnings, errors,
                        and informational messages will be reported.
                        If set to "2", all warnings, errors,
                        informational and debug messages will be reported.
--include-events INCLUDE_EVENTS [INCLUDE_EVENTS ...],
                    A list of events name to include in the plot.
                    If none is passed then all events will be included.
                    Must be less than 15 events.
--event_column EVENT_COLUMN,
                    Name of the column containing the events.

BIDS FILTERS:
Filters to customize PyBIDS get() as key=value pairs

--filter-events FILTER_EVENTS [FILTER_EVENTS ...],
                        (default: suffix=events extension=.tsv)

INPUT WILDCARDS:
File path entities to use as wildcards in snakemake

--wildcards-events WILDCARDS_EVENTS [WILDCARDS_EVENTS ...],
                        (default: subject session acquisition task run)

PATH OVERRIDE:
Options for overriding BIDS by specifying absolute paths that include wildcards,
e.g.: /path/to/my_data/{subject}/t1.nii.gz

--path-events PATH_EVENTS, --path_events PATH_EVENTS

group Level

usage: bidsgnostic_layout [-h]
                          [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
                          [--plot_by PLOT_BY [PLOT_BY ...]]
                          [--log_level {0,1,2}]
                        bids_dir output_dir {group}

Group level diagnostic tool for BIDS datasets.
Plots the number of files per participant / session per:
    - datatype,
    - datatype / task,
    - datatype / task and split by any other BIDS entity.

positional arguments:

bids_dir
output_dir
{group}

options:

-h, --help
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
--log_level {0,1,2}
--plot_by PLOT_BY [PLOT_BY ...]
                        BIDS entity to split plots by.