Help processing Bruker hepatic phantom data in LCModel

Ask Anything!
1

Hello everyone,
I am currently working with hepatic phantom data acquired on a 9.4T Bruker scanner, and I would like to process them in LCModel.

Since I am new to this area, I would really appreciate any guidance regarding:

  • The recommended workflow to convert Bruker data into a format compatible with LCModel (.RAW).
  • Tools or scripts that can help with the conversion
  • Practical tips to ensure acquisition parameters are correctly transferred and to avoid common errors.

I am also attaching an image showing the folder structure of my data, so you can see how they are organized. Any suggestions, guidance, or references would be very helpful for moving forward with my project.

image
image1384×732 43.7 KB

image
image1356×721 40.8 KB

2

Hi there,

For converting Bruker files to .raw, the FID-A toolbox seems like a good option.

For a big preclinical multi-site project CoMP-MRS, we have recently completely re-written the FID-A loader. You can find this new file io_loadspec_bruk_new here - I expect that it’ll eventually make its way back into the main FID-A repository (@JamieNear).

After loading, you’ll probably want to do some pre-processing - again, get some inspiration from the pipeline we’ve pre-built for the CoMP-MRS project.

At the end, you can use the FID-A function io_writelcm to create a .raw file.

Now you’ll still need to write good LCModel control files and have a basis set - let’s get back to that once you have the LCModel writing sorted out.

Cheers,
Georg

1 Like