As you can see, it took a really long time to model the data, and were getting these messages throughout (I used io_LCMMakeBasis to convert a 7T basis file to .mat…maybe an issue happened there)
Any help would be greatly appreciated. I am not super well-versed with MRS processing, so am hoping there is something I’m missing. I am also attaching my test job file.
Thank you so much,
Ally LongGluCESTJob.m (6.1 KB)
Just shared a Box folder with your email. Thank you so much for your help, and let me know if there is anything else you need. Attaching Box folder link.
I finally had a chance to look at the data. There were a few issues when looking at it:
Are you sure that you have shared the correct DCM files? I have tried to open them, but I am unable to read them. When I look at them with another DCM reader, it says that they are not an MRS SOP class. I managed to use the RDA files instead. SO I would opt for the RDA files if you have them for all datasets.
I had to modify the BASIS.mat file because we have a different definition for the center frequency and all the spectra were incorrectly shifted. I have uploaded the modified file to the box folder.
Similarly, I modified the .basis file to match the Osprey naming convention so that you can use the LCModel wrapper in Osprey for fitting.
The data itself looks great! The LCM results when using Osprey’s native LCM algorithm were not as good as I hoped them to be. We have mostly optimized everything for 3T MRS though. Could you create a basis set with a slightly broader linewidth? This might help the Osprey’s native LCM algorithm.
I have also modeled them using the LCModel wrapper in Osprey. To do that, you can change the fit method to ‘LCModel’. This way, Osprey takes care of the preprocessing and tissue correction and automatically uses LCModel for the fitting. This should give you the estimates you want for your analysis.
Let me know if you have any other questions and sorry for the delay.
