install_build_Analysis_LCModel

[Neda]

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:

Building LCModel

Dear all, Following the release of the LCModel source code I was able to get a successful build on Ubuntu 20.04 gcc version 9.3.0. First step is to install gfortran if you don’t already have it: sudo apt install gfortran download the source code from: LCModel's home page and unzip: unzip source.zip -d lcmodel_src cd lcmodel_src patch the code to overlook a failing internal check, “ILLOGICAL INITIA 5” - see LCModel manual, compile and link: sed '2429d' LCModel.f > LCModel_patched.f gfortr…

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)

[admin]

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

[Neda]

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

[admin]

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).