Dear community
I tried running LCModel on my windows machine (12th Gen Intel(R) Core™ i5-12500H 2.50 GHz, 16GB RAM) using WSL Ubuntu. However, after selecting the water suppressed/unsuppressed files and basis file, the gui stays blank and I get a message that
LCModel execution has started.
Click on “Next Analysis” to prepare another analysis with LCMgui.
It been more than one day running, without any result. Has anyone experienced something similar? I would greatly appreciate your feedback
Thanks
Hm. It’s odd that the GUI runs but the core binary doesn’t.
I’d suggest you try re-compiling the LCModel binary from source (see instructions here and discussion here); note that you can also compile the source directly for Windows/Mac so you don’t have to go the extra mile via WSL. The only downside is that you can’t use the GUI (which is not provided in source), but honestly it’s awfully clunky anyway, and I strongly recommend not using it in the first place, but rather to learn to write valid control files (see LCModel manual Section 5.3) which makes batching a lot easier.
Dear @admin
I followed the manual and reached to this point, where I am not sure how to solve this error.
The code is: 1 FATAL ZEROVX 5
which corresponds to this message in the manual
(FATAL) Error trying to read time data in FILRAW.
Hints: In FILRAW, check that the time data correspond to FMTDAT. Does the
file size correspond to your input NUNFIL, or (with multi-voxel data) with
NDSLIC, NDROWS, NDCOLS?
my NUNFIL=1024
and for FMTDAT I have: FMTDAT=‘(2E15.6)’
I got 1024 from my parameter file and I got 2E15.6 from the manual (I tried changing NUNFIL to 2048, but it did not worked)
How are you creating/writing out your .raw files? I think they need to follow a fairly tight format, especially for writing out the actual data. Here’s how we do it.
You cannot just rename RDA files into .RAW. They are completely different formats. LCModel is extremely picky and super-sensitive to the ways that .control and .raw files are written, and you need to follow the instructions in the manual 100%.
One way to do this would be to load the RDA files with io_loadspec_rda of the FID-A toolbox (MATLAB) and then write them out to .RAW again with io_writelcm. The functions are fairly trivial so if you need to re-write in Python you should be able to do that. I’m not sure but FSL-MRS might also have a function to write processed .nii back to .raw
Dear @admin
Thank you so much for your support! I’m excited to share my first LCModel plot, and as a second-year undergrad, I wouldn’t have learned this much without this forum.
Please see the plot attached. I have simulated the basis file using the MRScloud checking the metabolites present in my phantom. I would greatly appreciate your feedback on plot quality.
I can’t make sense of your data. There are many peaks that look out of place, and therefore the fit struggles.
I’m not sure you got your .RAW conversion right. Please describe exactly what you do between steps, it’ll make it easier to solve.
(Furthermore, the basis set does not contain enough components (what is the content of your control file?), but that’s not the first problem we’ll need to address)
Thanks for your feedback
I think a reason for a poor fit is the simplicity of control file. I only used hte suppressed raw file and did not used the unsuppressed file (Initially I just wanted to make sense of software operation, thats why I tried to keep it as simple as possible). The second image is from the datasheet of the phantom I used, as I saw it contains 7 metabolites, which I selected during basis simulation in MRScloud. I think my aim should be to get the numbers matching with the datasheet.
Don’t waste time on phantom data. Your numbers won’t match because you would need to do a full relaxation correction, and for that you’d need to measure the relaxation times of water and metabolites in this specific phantom. This is not feasible.
The main problem at this point is your data. Your spectrum does not look like the spectrum from this phantom needs to look like. Again, please describe how you create the .RAW file, this is key to understanding what’s going wrong.
