Creation of Bval bvec files

Dear @Nikita.Beliy

Could you add an example about how to create multiple bval/bvec files within a session?

Use case:

• in some protocols (COGNAP, IRONSLEEP, STR7T, etc), on top of the regular DWI sequence, there is an additional sequence with reverse PA. Although the bval/bvec files associated to that additional sequence are trivial (bval=0, bvec=0) and thus easy to create manually, it would be nice to be able to create them when bidsifying. Current issue:
• in most examples of the prepare_plugin I have seen, the bval/bvec variables are declared (global) and initialised in the SessionEP function. Then filled in the FileEP function and written in a file in the SequenceEndEP.
• with this current implementation, the bval/bvec variables contain the values for all the DWI sequences (regular+additional).

Having an example about how to proceed to have a separated bval/bvec file for each DWI sequence would ease the project-specific plugin implementation.

Thank you.

Cheers,

Greg

assigned to @Nikita.Beliy

These reverse PA files are not 'dwi' but 'fmap' (peopolars), that do not require bval/bvec. If you want to keep them with dwi, I think the same read_bval/bvec plugin functions should work.

Everything in plugin is responsibility of user. Provided files are the examples. Retrieval of bval/bvec values from metadata is too sequence dependent to integrate into main bidsme code.

I don't remember why I keep all bval/vec in memory, but probably it's because for CRC data, for each session, all nifti files are kept in one folder, so technically for bidsme they belong to the same acquisition. An alternative would be to detect a protocol name change in RecordingEP, an write bval/bvec at ths point. But it could be dangerous if files in source do not follow acquisition order, and maby error prone. If you can find a better way to extract bval/bvec, I will be happy to include them into template/examples.