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Configs

Global files

Nipoppy requires two global files for specifying local data/container paths and recruitment manifest.

Global configs: global_configs.json

  • This is a dataset-specific file and needs to be modified based on local configs and paths
  • This file is used as an input to all workflow runscripts to read, process and track available data
  • Copy, rename, and populate sample_global_configs.json
  • This file contains:
    • Name of the Nipoppy dataset (DATASET_NAME, e.g., PPMI)
    • Path to the Nipoppy dataset (DATASET_ROOT)
    • Path to a local CONTAINER_STORE comprising containers used by several workflow scripts
    • Path to a Singularity executable (SINGULARITY_PATH)
    • Path to a TemplateFlow directory, if using fMRIPrep (TEMPLATEFLOW_DIR)
    • List of session IDs (SESSION, for MRI data) and visit IDs (VISITS, for tabular data)
    • Containers + versions for BIDS conversion: HeuDiConv, BIDS validator (BIDS)
    • List of processing pipelines + versions (PROC_PIPELINES)
    • Information about tabular data (TABULAR)
      • Version and path to the data dictionary (data_dictionary)

Suggestion

Although not mandatory, for consistency the preferred location would be: <DATASET_ROOT>/proc/global_configs.json.

Sample global_configs.json

{
    "DATASET_NAME": "MyDataset",
    "DATASET_ROOT": "/path/to/MyDataset",
    "CONTAINER_STORE": "/path/to/container_store",
    "SINGULARITY_PATH": "singularity",
    "TEMPLATEFLOW_DIR": "/path/to/templateflow",

    "SESSIONS": ["ses-1","ses-5","ses-7","ses-9","ses-11"],

    "BIDS": {
        "heudiconv": {
            "VERSION": "0.11.6",    
            "CONTAINER": "heudiconv_{}.sif",
            "URL": ""
        },
        "validator":{
            "CONTAINER": "bids_validator.sif",
            "URL": ""

        }
    },

    "PROC_PIPELINES": {
        "mriqc": {
            "VERSION": "",
            "CONTAINER": "mriqc_{}.sif",
            "URL": ""
        },
        "fmriprep": {
            "VERSION": "20.2.7",
            "CONTAINER": "fmriprep_{}.sif",
            "URL": ""
        },
        "freesurfer": {
            "VERSION": "6.0.1",
            "CONTAINER": "fmriprep_{}.sif",
            "URL": ""
        }
    }
}

Participant manifest: manifest.csv

  • This list serves as the ground truth for subject and visit (i.e. session) availability
  • Create the manifest.csv in <DATASET_ROOT>/tabular/ comprising following columns
    • participant_id: ID assigned during recruitment (at times used interchangeably with subject_id)
    • visit: label to denote participant visit for data acquisition (e.g. "baseline", "m12", "m24" or "V01", "V02" etc.)
    • session: alternative naming for visit - typically used for imaging data to comply with BIDS standard
    • datatype: a list of acquired imaging datatype as defined by BIDS standard
    • bids_id: this is the participant_id after removing any non-alphanumeric character (e.g. "-" or "_") and attaching the sub- prefix. participant_id and bids_id in the manifest are used to link tabular and MRI data
  • New participant are appended upon recruitment as new rows
  • Participants with multiple visits (i.e. sessions) should be added as separate rows

Sample manifest.csv

participant_id visit session datatype bids_id
001 V01 ses-01 ["anat","dwi","fmap","func"] sub-001
001 V02 ses-02 ["anat"] sub-001
002 V01 ses-01 ["anat","dwi"] sub-002
002 V03 ses-03 ["anat","dwi"] sub-002