BIDS Ready Protocols

How to name your protocols so they are easily converted to BIDS format

BIDS Naming Pattern

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.

Color coded examples of BIDS compliant protocols

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 (_)

Additional Sample Protocols

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

Important considerations

Scouts and Localizers

All scout and localizer sequences need to have a scout label. For example:

• anat-scout_acq-localizer

• anat-scout_acq-aascout

Scout series will remain in the sourcedata directory of your bids output, but will not be present in your anat folder.

Incompatible symbols

Do not use "+", "_", "-" or "." within SESID, TASKID, ACQLABEL, RUNID. The only exception is the use of run+

Naming Runs

To indicate runs in your protocol, without explicitly indicating the run number, simply label the run as run+

Cancelled Runs

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

Functional runs must have _task- field defined

MEMPRAGE

You can choose (on the scanner) whether to send each individual echo along with the RMS image. Regardless, this data should now be converted appropriately to BIDS format.

Fieldmaps

Currently the fieldmaps collected with our Siemens scanner use the "old way" described here

Scanner derivatives

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)