install_build_Analysis_LCModel

Hi Dear expert

I am new in LCmodel and MRS analysis! but i have some question:

I have a data by GE scanner from muscle, and I installed my LCModel based on following commands on UBUNTU20.04:

./install-lcmodel
mkdir -p $HOME/.lcmodel/basis-sets
touch $HOME/.lcmodel/basis-sets/dummy.basis
touch $HOME/.lcmodel/license
cd $HOME/.lcmodel
./lcmgui

and build with these commands from:

sudo apt install gfortran
unzip source.zip -d lcmodel_src cd lcmodel_src
sed ‘2429d’ LCModel.f > LCModel_patched.f gfortran -c -fno-backslash -fno-f2c -ffast-math -O2 -ffpe-summary=none -Wuninitialized -std=legacy -fall-intrinsics LCModel_patched.f gfortran -s -static LCModel_patched.o -o lcmodel

Now:

  1. I use bias file from this Basis sets that I dont know it is true or not?!
  2. I analyze my data by default parameter and get a PS report file that I attached to email.

Would you please help me on analysis by LCModel?

Best,
Neda
ps.pdf (19.1 KB)

Hi Neda,

You have two options:

  1. If you want to use the original (pre-compiled) binaries, follow the installation instructions in the manual, then run touch $HOME/.lcmodel/license as per the LCModel homepage. You will need to include key = 210387309 in every control file that you create.

  2. You can follow the compilation instructions in the thread you linked. @martin has updated the recommended instructions since his initial post to improve numerical agreement with Provencher’s pre-compiled version, see here:
    Building LCModel - #9 by martin
    and
    Building LCModel - #13 by martin
    You will still need to add the key = 210387309 to every control file, but @alex has figured out a way to hack the source code to bypass this key check altogether.

You should not “mix and match” the two methods.

Edit: Assuming this is short-TE proton data, it looks like you have data with a very poor linewidth. Is this data representative of your entire dataset?

Edit2: There are specific settings for muscle spectra (sptype = muscle-4) which use an internal basis set to include IMCL and EMCL. The manual has pretty extensive documentation on this. Don’t use an externally provided separate basis set.

Georg

Hi again,

Thanks for reply.
I built my lcmodel by following @martin instruction.
now when i run ./lcmodel it gets back this error

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f38b544b680 in ???
#1 0x7f38b544a885 in ???
#2 0x7f38b4ac2f0f in ???
#3 0x7f38b544ad90 in ???
#4 0x55df65fe3a9e in mycont_
#5 0x55df66022254 in MAIN__
#6 0x55df65f8064e in main
Segmentation fault (core dumped)

Why? :((

Thanks in advance

Neda

Can you post the exact sequence of commands that you have run to compile, and the exact command you have run to cause this error? You can’t run ./lcmodel without an argument, you need to provide the control file as the argument (see chapter 5 in the manual).