auto-align transformation matrix in bids jason sidecar file

[Proulx-S]

I'm using auto-align on Siemens to ensure (prospectively) that my single-slice fMRI is stable in brain-space across a session. This means the scanner space slice prescription is never the same from one run to the other. For further retrospective motion correction, scanner-space slice prescriptions need to match. It is surprisingly difficult to copy slice prescription info from one header to the other without breaking anything. With the auto-align matrix on hand, one could just apply its inverse at the very beginning. I'm sure there are other work-around but having the matrix there in the .jsn seems the cleanest.

Thanks for the good work and
Have a great day!
Sébastien

[marcelzwiers]

I'm not sure what you want to say, do you mean that BIDScoin could do something here? It seems to me that this is a discussion you better have with the dcm2niix developer, as this is where the json-files are created in the first place?
https://github.com/rordenlab/dcm2niix

[Proulx-S]

You are right! This would be most elegantly handled by dcm2niix. I actually did ask the developers and they so far pointed me to the BIDS team (rordenlab/dcm2niix#944). So I did query the BIDS team here bids-standard/bids-specification#2141.