fixmeta - Man Page

fixmeta [-h] [-p LABEL [LABEL ...]] [-b NAME] bidsfolder pattern metadata

A bidsapp that can change or add metadata in BIDS data repositories. The fixmeta app supports the use of special bidsmap features, such as dynamic values to use source data attributes or properties, or to populate `IntendedFor` and `B0FieldIdentifier`/`B0FieldSource` values

bidsfolder

The BIDS root directory that needs fixing (in place)

pattern

Globlike recursive search pattern (relative to the subject/session folder) to select the json sidecar targets that need to be fixed, e.g. '*task-*echo-1*'

metadata

Dictionary with key-value pairs of metadata that need to be fixed. If value is a string, then this metadata is written to the sidecars as is, but if it is a list of `old`/`new` strings, i.e. `[old1, new1, old2, new2, ..]`, then the existing metadata is re-written, with all occurrences of substring `old` replaced by `new`

-p LABEL [LABEL ...], --participant LABEL [LABEL ...]

Space separated list of sub-# identifiers to be processed (the sub-prefix can be left out). If not specified then all participants will be processed

-b NAME, --bidsmap NAME

Selects a custom study bidsmap file for extracting source data properties and attributes. If the bidsmap filename is just the base name (i.e. no "/" in the name) then it is assumed to be located in the current directory or in bidsfolder/code/bidscoin. Default: bidsmap.yaml or else the template bidsmap

examples:
 fixmeta myproject/bids func/*task-reward1* '{"TaskName": "Monetary reward paradigm 1"}'
 fixmeta myproject/bids *acq-reward1* '{"B0FieldIdentifier": ["<<", "_", ">>", ""], "B0FieldSource": ["<<", "_", ">>", ""]}'
 fixmeta myproject/bids fmap/*run-2* '{"IntendedFor": "<<task/*run-2*_bold*>>"}' -p 001 003

Marcel Zwiers <m.zwiers@donders.ru.nl>