Frequently asked questions

How to change which files are downloaded / copied?

This is uses a JSON bids-filter file to specify the files to be downloaded for each dataset type.

The file is organized by dataset type and then list the “suffix groups” to be downloaded / copied for each dataset.

{
  "dataset_type": {
    "suffix_group": {
      "datatype": "func",
      "suffix": "bold",
      "ext": "nii*"
    }
  }
}

Each suffic group MUST have:

• "datatype"

• "suffix"

• "ext"

Those entries support typical glob pattern (like * or ?…).

The default filter file is located at cohort_creator/data/bids_filter.json.

{
    "raw": {
        "bold": {
            "datatype": "func",
            "task": "*",
            "suffix": "bold",
            "ext": "nii*"
        },
        "events": {
            "datatype": "func",
            "task": "*",
            "suffix": "events",
            "ext": "tsv"
        },
        "t1w": {
            "datatype": "anat",
            "suffix": "T1w",
            "ext": "nii*"
        },
        "t2w": {
            "datatype": "anat",
            "suffix": "T2w",
            "ext": "nii*"
        },
        "fmap": {
            "datatype": "fmap",
            "suffix": "*",
            "ext": "nii*"
        }
    },
    "mriqc": {
        "bold": {
            "datatype": "func",
            "suffix": "bold",
            "ext": "json"
        },
        "t1w": {
            "datatype": "anat",
            "suffix": "T1w",
            "ext": "json"
        },
        "t2w": {
            "datatype": "anat",
            "suffix": "T2w",
            "ext": "json"
        }
    },
    "fmriprep": {
        "bold": {
            "datatype": "func",
            "task": "*",
            "space": "*",
            "desc": "preproc",
            "suffix": "bold",
            "ext": "nii*"
        },
        "confounds": {
            "datatype": "func",
            "task": "*",
            "desc": "confounds",
            "suffix": "timeseries",
            "ext": "tsv"
        },
        "t1w": {
            "datatype": "anat",
            "space": "*",
            "desc": "preproc",
            "suffix": "T1w",
            "ext": "nii*"
        },
        "t2w": {
            "datatype": "anat",
            "space": "*",
            "desc": "preproc",
            "suffix": "T2w",
            "ext": "nii*"
        }
    }
}