fnirsapp_glm.json

{
    "name": "fNIRS Apps: GLM Pipeline",
    "description": "A GLM pipeline for fNIRS data",
    "author": "Robert Luke",
    "tool-version": "v0.3.4",
    "schema-version": "0.5",
    "command-line": "/run.py [InputDataset] [OutputLocation] [SubjectLabel] [SessionLabel] [TaskLabel] [ShortRegression] [ExportDrifts] [ExportShorts] [SampleRate]",
    "container-image": {
        "image": "ghcr.io/rob-luke/fnirs-apps-glm-pipeline/app:v0.3.4",
        "index": "ghcr.io",
        "type": "docker",
        "entrypoint": true
    },
    "inputs": [
        {
            "command-line-flag": "--input-datasets",
            "id": "input_datasets",
            "description": "The directory with the input dataset formatted according to the BIDS standard.",
            "name": "input-datasets",
            "optional": true,
            "type": "File",
            "value-key": "[InputDataset]"
        },
        {
            "command-line-flag": "--output-location",
            "id": "output_location",
            "description": "The directory where the output files should be stored.",
            "name": "output-location",
            "optional": true,
            "type": "File",
            "value-key": "[OutputLocation]"
        },
        {
            "command-line-flag": "--subject-label",
            "description": "The label(s) of the subjects(s) that should be analyzed. The label corresponds to sub-<subject_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.",
            "id": "subject_label",
            "name": "subject-label",
            "optional": true,
            "type": "String",
            "list": true,
            "value-key": "[SubjectLabel]"
        },
        {
            "command-line-flag": "--session-label",
            "description": "The label(s) of the session(s) that should be analyzed. The label corresponds to ses-<session_label> from the BIDS spec (so it does not include \"ses-\"). If this parameter is not provided all sessions should be analyzed. Multiple sessions can be specified with a space separated list.",
            "id": "session_label",
            "name": "session-label",
            "optional": true,
            "type": "String",
            "list": true,
            "value-key": "[SessionLabel]"
        },
        {
            "command-line-flag": "--task-label",
            "description": "The label(s) of the tasks(s) that should be analyzed. The label corresponds to task-<subject_label> from the BIDS spec. If this parameter is not provided all tasks should be analyzed. Multiple tasks can be specified with a space separated list.",
            "id": "task_label",
            "name": "task-label",
            "optional": true,
            "type": "String",
            "list": true,
            "value-key": "[TaskLabel]"
        },
        {
            "command-line-flag": "--short-regression",
            "id": "short_regression",
            "name": "short-regression",
            "optional": true,
            "type": "String",
            "value-choices": [
                "True",
                "False"
            ],
            "value-key": "[ShortRegression]"
        },
        {
            "command-line-flag": "--export-drifts",
            "id": "export_drifts",
            "name": "export-drifts",
            "optional": true,
            "type": "String",
            "value-choices": [
                "True",
                "False"
            ],
            "value-key": "[ExportDrifts]"
        },
        {
            "command-line-flag": "--export-shorts",
            "id": "export_shorts",
            "name": "export-shorts",
            "optional": true,
            "type": "String",
            "value-choices": [
                "True",
                "False"
            ],
            "value-key": "[ExportShorts]"
        },
        {
            "command-line-flag": "--sample-rate",
            "id": "sample_rate",
            "name": "sample-rate",
            "optional": true,
            "type": "Number",
            "value-key": "[SampleRate]"
        }
    ],
    "output-files": [
        {
            "id": "output_directory",
            "name": "BIDS derivatives directory",
            "optional": false,
            "path-template": "[OutputLocation]"
        }
    ],
    "suggested-resources": {
        "cpu-cores": 1,
        "ram": 1,
        "walltime-estimate": 60
    },
    "tags": {
        "domain": [
            "neuroimaging",
            "fnirs",
            "glm",
            "bids"
        ]
    },
    "error-codes": [
        {
            "code": 1,
            "description": "Crashed"
        }
    ],
    "custom": {
        "BIDSAppSpecVersion": "Draft"
    },
    "doi": "10.5281/zenodo.5886927"
}