search

physiopy / phys2bids

Python3 library to format physiological files in BIDS. At the moment, it supports Acqknowledge and Labchart. BrainHack participants, check the issues with the BrainHack labels!
https://phys2bids.readthedocs.io
Apache License 2.0
64 stars 45 forks source link

Add support for Siemens physiological recordings #339

Open smoia opened 3 years ago

smoia commented 3 years ago

Long story short, there is the possibility of acquiring physiological files with the MRI scanners. All the Siemens physiological converters I found are not being currently maintained (not a problem), and the files might be more straightforward to work with than expected (in the end, they are text files).

The two solutions I found are ostanley/physio2bids and tarrlab/physio2bids. They both don't have licenses, so technically we can't use any of the code reported there.

I'm tagging @ostanley and @pitchaim since they have been working on these files already. If you two would like to help us with this integration, we'd be glad to have you onboard! Alternatively, if you want to add a License that doesn't require us to change ours, we'd also be grateful for that!

tsalo commented 3 years ago

Doesn't cbinyu/bidsphysio support Siemens data? They have an MIT license.

smoia commented 3 years ago

Ah, that is true! It can be another implementation then - if anyone wants to dig their code for it!

vinferrer commented 3 years ago

Do we have a data example?

RayStick commented 3 years ago

Do we have a data example?

In my current study, I am collecting Siemens data physiological data (respiration and pulse) during BOLD and ASL scans, so will have data examples, and would like to see if I can start using phys2bids properly for the preprocessing of these recordings.

CesarCaballeroGaudes commented 3 years ago

@vinferrer there are also physio recordings available in BCBL based on the CMRR sequence, which follows the Siemens structure for physio files. You can also check this repo https://github.com/CMRR-C2P/MB