How to change my raw kspace data to ISMRMRD file format?

[Breeze-Zero]

Hi, thank you for doing these implementations, I have seen many test scripts, but they are too scattered, if I need to convert my data to ISMRMRD file format, is there a more complete process?

[hansenms]

What format are you converting from? You may want to look at some of the vendor specific converters.

[Breeze-Zero]

What format are you converting from? You may want to look at some of the vendor specific converters.

It is the data collected by myself. At present, I have temporarily converted the original data into K-space data saved by MAT, and I want to convert it into ISMRMRD File Format for future public sharing. But actually I am not very familiar with ISMRMRD File Format, and I am worried that the final result will be different from the standard, which will cause inconvenience to others.

[hansenms]

Not totally sure what "collected by myself" means? I am assuming it was collected by some instrument in some file format? My reason for asking is that most of the time when converting data, the hard part is getting all the parameters out of the original format. Writing the ISMRMRD format is usually easier. Nevertheless, you could look at something like this simulator: https://github.com/ismrmrd/ismrmrd-python-tools/blob/master/ismrmrdtools/simulation.py if you are looking for something written in python.

[Breeze-Zero]

Thank you for your prompt reply. In short, I converted the raw data collected by the machine into the K-space data .mat File (x, Y, Coil,slice) and the .dcm File reconstructed by the machine's own software algorithm. Now I want to use these two to build the ISMRMRD File Format.

[hansenms]

When you say you "converted the raw data collected by the machine", I am assuming that was in some sort of format. If this is a well known machine (Siemens, GE, Philips, Bruker, etc.) then there are converters you can start with. Check the repos in this org. Collecting the k-space lines in a matrix may mean that you have lost some of the information needed for proper ISMRMRD representation. Specifically, ISMRMRD is stored profile by profile to ensure it captures acquisition order. This may not be possible with your representation. Either way, check simulator tools for examples of how to generate data from scratch and hopefully you can fit your data into this pattern.

[seogier]

I've also struggled with writing my own ISMRMRD files. The best resource I've found, so far, is this example https://github.com/ismrmrd/ismrmrd-python-tools/blob/master/generate_cartesian_shepp_logan_dataset.py