I am running into a processing error on Osprey for Siemens MEGA-PRESS data. I have scanned an MRS phantom (Braino GE) recently. There is no GABA in this particular phantom, but I am just testing the sequence and working with what I got until I can get a better phantom.
I am also attaching my job file. I am unsure if my input parameters are correct or if there is a different issue? My main question is what kind of input is Osprey expecting for this data?
In addition, I have some Siemens csi slaser data but I see Osprey doesn’t yet have multivoxel processing capability for this. Even though Im running into errors, this seems like the best package available and I would love to do all of my processing using one software. Is there any update for siemens multivoxel data processing?
Thank you so much and please let me know if there is anything else I can share to better answer this question!
Thanks for giving Osprey a shot! What’s the exact sequence and software version and what are the files you exported looking like - do you have a single RDA file, exactly three, or one RDA file per transient?
CSI analysis is under development but certainly not yet in the main branch - we unfortunately don’t really have a timeline for it as it’s not our current primary focus of development.
Thank you for the quick reply! I am running Siemens WIP_859G (mega-press). The files I exported was a single RDA file, I think the difference spectra.
I will be exporting single averages today, I just acquired that data yesterday.
I also have access to twix export which I will try with Osprey next.
However, the .rda data is giving me an issue. I am going to proceed with the raw data but I am just wondering what the issue might be for the .rda?
So, I exported single averages from the WIP_859 siemens sequence, but the program crashes on line 75 in osp_onoffClassifyMEGA.m. It seems that the code expects the “spec” object to be a M x 2 matrix, but for me it turns out to be an M x 1 matrix. The same issue occurs if I run the three RDA files which I exported from when running the sequence without selecting the single-averages option. Essentially, my question is, what is the structure that Osprey is expecting for the RDA data, and would you know why my specs are different? Perhaps it is something wrong with my acquisition? In addition, is Osprey processing each file alone or does it concatenate all of the single averages, for example?
As a side note, exporting single averages is quite cumbersome. There were > 300 single RDA files to export (I was unable to export them all as there is no batch export option on the scanner). Is that what is expected/how do you recommend exporting and dealing with single average data?
I am a novice to MRS, so any and all input is greatly appreciated! Thank you so much