How to use advanced commands and configuration

These optional configurations could be insert in the configuration file at the same level as the "descriptions" entry.

{
    "searchMethod": "fnmatch",
    "caseSensitive": true,
    "defaceTpl": ["pydeface", "--outfile", "dstFile", "srcFile"],
    "description": [
        ...
    ]
}

searchMethod

default: "searchMethod": "fnmatch"

fnmatch is the behaviour (See criteria) by default and the fall back if this option is set incorrectly. re is the other choice if you want more flexibility to match criteria.

caseSensitive

default: "caseSensitive": "true"

If false, comparisons between strings/lists will be not case sensitive. It's only disabled when used with "searchMethod": "fnmatch".

defaceTpl

default: "defaceTpl": None

!!! danger The anonymizer option no longer exists from v2.0.0. It is still possible to deface the anatomical nifti images.

For example, if you use the last version of pydeface, add:

"defaceTpl": "pydeface --outfile {dstFile} {srcFile}"

It is a template string and dcm2bids will replace {srcFile} and {dstFile} by the source file (input) and the destination file (output).

dcm2niixOptions

default: "dcm2niixOptions": "-b y -ba y -z y -f '%3s_%f_%p_%t'"

Arguments for dcm2niix

compKeys

default: "compKeys": ["SeriesNumber", "AcquisitionTime", "SidecarFilename"]

Acquisitions are sorted using the sidecar data. The default behaviour is to sort by SeriesNumber then by AcquisitionTime then by the SidecarFilename. You can change this behaviour setting this key inside the configuration file.

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Last update: 2023-07-06