Bids support for fetal MRI scans

1

Dear all,

Do you have any information about BIDS standard for raw fetal MRI data ?

Fetal MRI data description

Fetal MRI data are essentially anatomical MRI T2 data composed of several sequences (e.g. HASTE, or TrueFisp) acquired according to several orientations (e.g. axial, coronal, sagittal, transverse). Usually there are three different orientations and each orientation can be repeated several times (e.g. 1 coronal acquisition and 2 sagittal acquisitions). Also different in-line (console) processing can be applied (e.g, motion correction, distortion correction)

Do you think such kind of data could be represented using the usual MRI bids keywords (e.g. run, desc) ?

Thank you in advance,

2

Dear Alexandre,

Yes, raw fetal MRI could be indeed represented using usual MRI BIDS keywords, which is indeed the format adopted by the mialsupersolutiontoolkit (MIALSRTK).

You can have a basic dataset example illustrated here.

In this example, only the entity “run-” is used to identify the different scans.

If you wish to encode the type of sequence used in the filename, you could use for instance:

sub-01/anat/
  sub-01_scans.tsv
  sub-01_scans.json
  sub-01_acq-HASTE_run-1_T2w.nii.gz
  sub-01_acq-HASTE_run-1_T2w.json
  sub-01_acq-HASTE_run-2_T2w.nii.gz
  sub-01_acq-HASTE_run-2_T2w.json
  sub-01_acq-HASTE_run-3_T2w.nii.gz
  sub-01_acq-HASTE_run-3_T2w.json
  sub-01_acq-TrueFisp_run-1_T2w.nii.gz
  sub-01_acq-TrueFisp_run-1_T2w.json
  sub-01_acq-TrueFisp_run-2_T2w.nii.gz
  sub-01_acq-TrueFisp_run-2_T2w.json
  sub-01_acq-TrueFisp_run-3_T2w.nii.gz
  sub-01_acq-TrueFisp_run-3_T2w.json

where a column “orientation” that specifies the orientation for each (acq-<label> , run-<label>) pair is used the scans file (See here).
The scans.tsv should look like:

acquisition    run    orientation
HASTE    1    axial
HASTE    2    sagittal
HASTE    3    coronal

By looking at the latest BIDS specs, it states for the run entity (See here) that:

If different entities apply, such as a different session indicated by ses-<label>, or different acquisition parameters indicated by acq-<label>, then run is not needed to distinguish the scans and MAY be omitted.

In this case, the following would be more adequate in the context of fetal MRI:

[…], then run MAY NOT be needed to distinguish the scans and MAY be omitted.

In the current version of BIDS specs, it is not possible to use the _desc-<label>_ entity to encode the acquisition direction, as this entity is intended ONLY FOR DERIVATIVES data (See here)

I am not sure to fully understand what you mean by

Also different in-line (console) processing can be applied (e.g, motion correction, distortion correction).

Are these operations performed during acquisition at the scanner level, or as a post-acquisition processing steps, such as in MIALSRTK to perform super-resolution reconstruction?

In the second case, data is considered as derivative and not raw, and should follow as close as possible the BIDS derivatives extension for MRI data. For now, the documentation of MIALSRTK outputs can give you an example of the organization and naming of the produced outputs (See here).

Hope this helps!

Best,
Sebastien

3

Dear Sebastien,

Thank you very much for your quick and complete answer. I will have a look at the examples you mention and adapt to the suggested bids formatting

Blockquote
Are these operations performed during acquisition at the scanner level, or as a post-acquisition processing steps, such as in MIALSRTK to perform super-resolution reconstruction?

These operations are indeed performed during the acquisition.In the case of MRI scans with highly heterogeneous processing performed during acquisition (e.g. with/without manufacturer 2D/3D distortion correction, normalization) what would you recommend ?

Thanks again for your help and your time.
Best,
Alexandre