DSC and DCE perfusion mris corresponding suffix in bids format

[MeryemABBAD]

Hello,

We are trying to convert a brain tumor dataset into the bids format. This dataset has DSC perfusion mris. However, in the bids documentation I only found an equivalent for asl perfusion mri and none for DSC or DCE. Should we add a suffix dsc or dce even though it will generate the error that it is not validated by bids?

Thank you!

Meryem, @RaphaelMaser, @adhusch

[effigies]

This comes up periodically for OpenNeuro, so I have some draft text for a FAQ: https://github.com/OpenNeuroOrg/openneuro/issues/2845

[...] there are times when scans are useful to include in a BIDS dataset even though those data types are not yet fully standardized.

For those cases, we recommend reviewing the list of BIDS Enhancement Proposals (BEPs). If your scan type appears in that list, we suggest following the naming and metadata conventions put forward in the corresponding BEP. The resulting files can be listed in a .bidsignore file to instruct the BIDS validator to ignore them.

If there is no BEP, but the files are still important for understanding or processing the dataset, then the BIDS standard states:

Additional files and directories containing raw data MAY be added as needed for special cases. All non-standard file entities SHOULD conform to BIDS-style naming conventions, including alphabetic entities and suffixes and alphanumeric labels/indices. Non-standard suffixes SHOULD reflect the nature of the data, and existing entities SHOULD be used when appropriate. For example, an ASSET calibration scan might be named sub-01_acq-ASSET_calibration.nii.gz.

Non-standard files and directories should be named with care. Future BIDS efforts may standardize new entities and suffixes, changing the meaning of filenames and setting requirements on their contents or metadata. [...]

I don't know enough about DSC/DCE to know whether they could be appropriately labeled as something that already exists. It appears that DSC at least is a T2* contrast with a contrast-enhancing agent. If they are multi-volume, it might be sensible to put them under func/sub-XX_task-rest_ce-<label>_bold.nii.gz.

If these need to be specified, it would be good to go through the MRI sections of BIDS and see what metadata fields may already exist that would be necessary, desired, or possible to encode for the images to be meaningfully interpreted. Then it would be good to find DICOM tags that correspond to these fields that are present in the data as they come from the scanner, so we can ensure conversion with tools like dcm2niix.

Depending on the scope of these, it may be possible to create a simple PR, or it may be necessary to create a BEP (see BEP Guide).

[MeryemABBAD]

Dear Chris,

Thank you very much for your answer. I think that the DSC or DCE MRI fall into the same category as Arterial Spin Labelling (under perfusion MRI). However these are distinct modalities and I think that the procedure might be the same as BEP005 (https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c/edit#heading=h.prrzvwchfio6 ) for ASL. Therefore, if I understood correctly, a new BEP would be needed for DSC MRIs. The idea would be to name the DSC file: under the perf metadata "sub_XX_ses_XX_dsc.nii.gz". If this is necessary, we are going to proceed with the BEP following the instructions.

Thank you,

Best regards,

Meryem

[nhuneke]

Hi,

We are using DCE MRI locally for a number of projects and I would like to BIDS-ify our datasets. I agree these should fall under perf/ but currently there is no specification for DCE or DSC. I was just wondering whether you started a BEP for this?

Thanks, Nathan