BIDS Ready Protocols
How to name your protocols so they are easily converted to BIDS format
We provide custom code (xnat-tools package) to export your XNAT imaging sessions to BIDS format. The process relies on naming your series in a BIDS friendly manner. If you are new to BIDS, it may be helpful to familiarize yourself with the BIDS Standard. We also provide a short overview of BIDS in this section.
When naming your series at the scanner you will need to think of the different parts that make up the BIDS name. More explicitly, the name of the series is composed of different parts that provide information about the sequence type (i.e, anatomical, functional, etc), task information, acquisition parameters, the run id, among others. The examples and diagram below show the parts of the BIDS name that you need to pay attention when naming your series at the scanner. These are only a subset of the full set defined by the BIDS specification. You can refer to the Entity Table of the BIDS specification for a full reference.
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Color coded examples of BIDS compliant protocols
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Table how to build series at the scanner for BIDS compliance
To create the final name, the different parts shown above are concatenated using underscores (_)
anat-scout_acq-aascout
anat-scout_acq-localizer
anat-T1w_acq-memprage
fmap_acq-greAP
func-bold_task-TSSblock_acq-2dot4mmSMS4TR1200AP_run+
anat-scout_acq-localizer
anat-scout_acq-aascout
anat-t1w_acq-memprage
func-bold_task-lum_run+
dwi_acq-122_dir-ap
dwi_acq-b0_dir-pa
All scout and localizer sequences need to have a
scout label. For example:anat-scout_acq-localizeranat-scout_acq-aascout
Scout series will remain in the
sourcedata directory of your bids output, but will not be present in your anat folder. Do not use "+", "_", "-" or "." within SESID, TASKID, ACQLABEL, RUNID. The only exception is the use of
run+To indicate runs in your protocol, without explicitly indicating the run number, simply label the run as
run+If run was canceled you will need to skip that series when calling the BIDS exporting code
xnat2bids. We encourage adding a note to that series in XNAT to indicate that the run was cancelled. This will improve bookkeeping and maintainability.Functional runs must have _task- field defined
Typically the scanner is configured to send the mutiple echoes and the RMS series. At the moment, BIDS does not support multi-echoes in the
anat category. When calling our xnat2bids software, please skip the multi-echo series. (This behavior may change in the future. See here for more details)Some sequences are derivatives of the scanner and are not yet handled by our
xnat2bids software smoothly. We recommend not exporting those sequences to BIDS at the moment. (This behavior may change in the future. See here for more details)Last modified 11mo ago