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Minor tweak
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marcelzwiers committed Mar 27, 2024
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2 changes: 1 addition & 1 deletion docs/bidsmap.rst
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Expand Up @@ -66,7 +66,7 @@ In case duplicated field maps are acquired (e.g. when a scan failed or a session

Fieldmaps: B0FieldIdentifier/B0FieldSource
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
According to the BIDS specification, within a subject folder, fieldmaps and their target scans can also be associated by way of `B0FieldIdentifier and B0FieldSource <https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#using-b0fieldidentifier-metadata>`__ tags. However, in practice if you acquire multiple scan session, fieldmaps are only associated with targets that were acquired within the same scan session. To achieve that you can add a special ``<<session>>`` dynamic value to your tags, which will be replaced with the session label during bidscoiner runtime. And similar to the IntendedFor value, you can append a colon-separated "bounding" term to the session tag, e.g. ``<<session:[0:3]>>`` to uniquely tag a fieldmap run (in the fmap folder) and three subsequent associated runs (e.g. in the func folder). So for instance, if you have ``{B0FieldIdentifier: pepolar_<<session>>}`` in your bidsmap metadata, then your actual output metadata in your ``ses-01`` subfolder will be ``{B0FieldIdentifier: pepolar_01}`` and in your ``ses-02`` subfolder it will be ``{B0FieldIdentifier: pepolar_02}``. Below, as an example, you can see the BIDS filetree for an acquisition with a single fieldmap and three subsequent functional runs that was interrupted after two runs and re-scanned, with ``mytag<<session:[0:3]>>`` as B0FieldIdentifier/Source bidsmap value. During bidscoiner runtime, when these bidsmap values are saved to the json sidecar files, then ``session`` is replaced by the session-label and ``:[0:3]`` is replaced by the fieldmap run-index)::
According to the BIDS specification, within a subject folder, fieldmaps and their target scans can also be associated by way of `B0FieldIdentifier and B0FieldSource <https://bids-specification.readthedocs.io/en/stable/04-modality-specific-files/01-magnetic-resonance-imaging-data.html#using-b0fieldidentifier-metadata>`__ tags. However, in practice if you acquire multiple scan session, fieldmaps are only associated with targets that were acquired within the same scan session. To achieve that you can add a special ``<<session>>`` dynamic value to your tags, which will be replaced with the session label during bidscoiner runtime. And similar to the IntendedFor value, you can append a colon-separated "bounding" term to the session tag, e.g. ``<<session:[0:3]>>`` to uniquely tag a fieldmap run (in the fmap folder) and three subsequent associated runs (e.g. in the func folder). So for instance, if you have ``{B0FieldIdentifier: pepolar_<<session>>}`` in your bidsmap metadata, then your actual output metadata in your ``ses-01`` subfolder will be ``{B0FieldIdentifier: pepolar_01}`` and in your ``ses-02`` subfolder it will be ``{B0FieldIdentifier: pepolar_02}``. This is further illustrated below, where you can see the BIDS filetree for an acquisition with a single fieldmap and three subsequent functional runs that was interrupted after two runs and re-scanned. The bounded B0FieldIdentifier/Source values used in the bidsmap were ``mytag<<session:[0:3]>>``. During bidscoiner runtime, ``session`` was replaced by the session-label and ``:[0:3]`` was replaced by the fieldmap run-index, after which the values were saved in the json sidecar files::

|-- fmap
| |-- sub-001_ses-01_run-1_magnitude1.json <- {B0FieldIdentifier: mytag<<ses01_1>>} (SeriesNumber = 01)
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