5.2. Running Jobs#

Once we have the code-less configuration file, we can use the command line interface to extract the features. This is achieved in a two-step process: run and collect.

The run command is used to extract the features from each element in the dataset. However, depending on the storage interface, this may create one file per subject. The collect command is then used to collect all of the individual results into a single file.

Assuming that we have a configuration file named config.yaml, the following commands will extract the features:

junifer run config.yaml

The run command accepts the following additional arguments:

  • --help: Show a help message.

  • --verbose: Set the verbosity level. Options are warning, info, debug.

  • --element: The element to run. If not specified, all elements will be run. This parameter can be specified multiple times to run multiple elements. If the element requires several parameters, they can be specified by separating them with ,. It also accepts a file (e.g., elements.txt) containing complete or partial element(s).

5.2.1. Example of running two elements:#

junifer run config.yaml --element sub-01 --element sub-02

You can also specify the elements via a text file like so:

junifer run config.yaml --element elements.txt

And the corresponding elements.txt would be like so:

sub-01
sub-02

5.2.2. Example of elements with multiple parameters and verbose output:#

junifer run --verbose info config.yaml --element sub-01,ses-01

You can also specify the elements via a text file like so:

junifer run --verbose info config.yaml --element elements.txt

And the corresponding elements.txt would be like so:

sub-01,ses-01

In case you wanted to run for all possible sessions (e.g., ses-01, ses-02, ses-03) but only for sub-01, you could also do:

junifer run --verbose info config.yaml --element sub-01

or,

junifer run --verbose info config.yaml --element elements.txt

and then the elements.txt would be like so:

sub-01

5.3. Collecting Results#

Once the run command has been executed, the results are stored in the output directory. However, depending on the storage interface, this may create one file per subject. The collect command is then used to collect all of the individual results into a single file.

Assuming that we have a configuration file named config.yaml, the following commands will collect the results:

junifer collect config.yaml

The collect command accepts the following additional arguments:

  • --help: Show a help message.

  • --verbose: Set the verbosity level. Options are warning, info, debug.