Running NiQuery¶

Command line interface¶

niquery¶

CLI for working with OpenNeuro BOLD runs.

Usage

niquery [OPTIONS] COMMAND [ARGS]...

aggregate¶

Aggregate NIfTI files listed in the input file into a new DataLad dataset.

Clones the corresponding OpenNeuro datasets, and downloads only those files listed towards the creation of the new dataset.

IN_FILENAME path NIfTI filename list filename

OUT_DIRNAME path Output dirname

NAME str Name of the dataset

Usage

niquery aggregate [OPTIONS] IN_FILENAME OUT_DIRNAME NAME

Options

-f, --force¶: Allow overwriting output files or writing to non-empty directories.

Arguments

IN_FILENAME¶: Required argument

OUT_DIRNAME¶: Required argument

NAME¶: Required argument

analyze¶

Analyze modality-specific files in datasets to extract relevant features.

Analyzes the modality-specific data files contained in the records of each dataset in the input directory. The suffix indicates what files will be analyzed. The features computed include the number of volumes of each file.

IN_DIRNAME path Input dirname

OUT_DIRNAME path Output dirname

SUFFIX str Modality suffix to consider

Usage

niquery analyze [OPTIONS] IN_DIRNAME OUT_DIRNAME

Options

--suffix <suffix>¶: Required Modality suffixes to consider

-f, --force¶: Allow overwriting output files or writing to non-empty directories.

Arguments

IN_DIRNAME¶: Required argument

OUT_DIRNAME¶: Required argument

collect¶

Collect datasets’ file information using the remotes and IDs read from the input file.

For each queried dataset, the list of files is stored in a delimiter-separated file, along with the ‘remote’, ‘id’, ‘filename’, ‘size’, ‘directory’, ‘annexed’, ‘key’, ‘urls’, and ‘fullpath’ features.

IN_FILENAME path Dataset list filename

OUT_DIRNAME path Output dirname

MODALITY str Modalities to consider

SPECIES str Species to consider

Usage

niquery collect [OPTIONS] IN_FILENAME OUT_DIRNAME

Options

--species <species>¶: Required Species to consider

--modality <modality>¶: Required Modalities to consider

-f, --force¶: Allow overwriting output files or writing to non-empty directories.

Arguments

IN_FILENAME¶: Required argument

OUT_DIRNAME¶: Required argument

index¶

Index existing dataset information from a remote server.

The remote server needs to offer a GraphQL API.

The ‘remote’, ‘id’, ‘name’, ‘species’, ‘tag’, ‘dataset_doi’, ‘modalities’, and ‘tasks’ features of the available datasets are stored in the output file using a delimiter-separated format.

REMOTE str Remote server name OUT_FILENAME path Output filename

Usage

niquery index [OPTIONS] REMOTE OUT_FILENAME

Options

-f, --force¶: Allow overwriting output files or writing to non-empty directories.

Arguments

REMOTE¶: Required argument

OUT_FILENAME¶: Required argument

select¶

Select relevant BOLD runs based on constraints.

Selects relevant fMRI BOLD runs based on the following set of constraints:

Criterion 1: no single dataset shall contribute more than a fraction of the total number of runs.

Criterion 2: each BOLD run shall have between a minimum and maximum number of timepoints (inclusive).

Results are stored using a delimiter-separated format.

IN_DIRNAME path Input dirname

OUT_FILENAME path Output data list filename

SEED integer Random seed. Use the format ‘YYYYMMDD’ for a date

Usage

niquery select [OPTIONS] IN_DIRNAME OUT_FILENAME SEED

Options

--total-runs <total_runs>¶

Number of total runs

Default:: 4000

--contr-fraction <contr_fraction>¶

Allowed contribution fraction for runs per dataset over the total runs

Default:: 0.05

--min-timepoints <min_timepoints>¶

Minimum number of BOLD timepoints per dataset

Default:: 300

--max-timepoints <max_timepoints>¶

Maximum number BOLD timepoints per dataset

Default:: 1200

-f, --force¶: Allow overwriting output files or writing to non-empty directories.

Arguments

IN_DIRNAME¶: Required argument

OUT_FILENAME¶: Required argument

SEED¶: Required argument