nipoppy extract

Note

This command calls the nipoppy.workflows.extractor.ExtractionRunner class from the Python API internally.

Logfiles for this command can be found in {{dpath_logs}}/extract.

nipoppy extract

Extract imaging-derived phenotypes (IDPs) from processed data.

nipoppy extract [OPTIONS] [DATASET_ARGUMENT]

Options

--dataset <dpath_root>

Path to the root of the dataset (default is current working directory).

Default:

PosixPath('/home/docs/checkouts/readthedocs.org/user_builds/nipoppy/checkouts/latest/docs/source')

--pipeline <pipeline_name>

Required Pipeline name, as specified in the config file.

--pipeline-version <pipeline_version>

Pipeline version, as specified in the config file.

--pipeline-step <pipeline_step>

Pipeline step, as specified in the config file (default: first step).

--participant-id <participant_id>

Participant ID (with or without the sub- prefix).

--session-id <session_id>

Session ID (with or without the ses- prefix).

--write-list <write_list>

Path to a participant-session TSV file to be written. If this is provided, the pipeline will not be run: instead, a list of participant and session IDs will be written to this file.

--simulate

Simulate the pipeline run without executing the generated command-line.

--layout <fpath_layout>

Path to a custom layout specification file, to be used instead of the default layout.

-n, --dry-run

Print commands but do not execute them.

-v, --verbose

Verbose mode (Show DEBUG messages).

Arguments

DATASET_ARGUMENT

Optional argument