What does LCModel bin2raw program do exactly?

[alex]

Hi @HfxCarlos,

@HfxCarlos

But so far, my results from manual lcmodel fitting are noticeably different that fully licensed LCmodel.

That’s interesting. Have you looked over the thread here?

Building LCModel

Hi all, Sorry to resurrect an old thread but I had a question about compiling LCModel on M1. I’ve been able to successfully run LCModel on my M1 Macbook-pro, Monterey 12.1, using two methods: GFortan 12.1 for Monterey - ARM, using locally-compiled LCModel version GFotran 10.2 for Catalina - INTEL, using Catalina-compiled LCModel binary in the Osprey repo For the compilation I followed @admin’s suggestion: gfortran -c -fno-backslash -fno-f2c -O3 -fall-intrinsics -std=legacy -Wuninitialized -…

There are a number of compiler optimisations which may lead to very slight deviations in some of the floating point operations, which could potentially accumulate to more substantial deviations – so perhaps that’s something to look into. Also I’m curious whether this was an M1/M2 macbook or an Intel system?

Regarding GE compatibility in future releases (beyond rev 30) – at some stage, we’ll likely need to move over to the ScanArchive format. I believe there may already be some work in this direction (@wclarke, @noeskera).

@HfxCarlos

If I understand how lcmgui works, it first calls the gelx/bin2raw preprocessor program that combines channels, transients and maybe a basic phase/freq correction before saving the data as a raw file and calling the lcmodel fitting tool with a basis set and control file.

Unfortunately being closed source it’s impossible to be certain exactly what bin2raw does, but I would say your understanding is basically correct – except, surprisingly, it doesn’t appear to be combining channels. What we usually see coming out (for single-voxel) is a single FID for each coil element, with differing phases. So it’s combining transients for each receiver separately, and apparently not doing much with the phase across elements (although perhaps within). It’s also not doing ECC: water reference is maintained explicitly for this purpose; it happens by default (but optionally) in the main lcmodel program.

Note that some of the combination (eg, adding transients across each full phase cycle) may happen on the scanner already, especially for standard PRESS sequences, if you haven’t explicitly asked the sequence not to do that.

There has been quite a lot of work towards improved spectral registration and automatic filtering of bad averages in recent years – I think it’s fair to assume that bin2raw has not been updated to take into account recent developments in that area. Robust spectral registration with modern methods implemented in FID-A/Gannet/FSL-MRS/Osprey or whatever other up-to-date tool you prefer will likely outperform these – at least for healthy brain tissue. For lesion and non-brain, this is not necessarily the case without further tuning.