The Laminar Cortex Model

Copyright (C) 2015-2017 Jiaxin Du.

This software implements the laminar cortex model, see

Du J, Vegh V, & Reutens DC, PLOS Compt Biol 8(10): e1002733; & NeuroImage 94: 1-11.

Compile

In Linux, the program can be compiled using GNU C++ compiler, for example,

g++ -o runlcm -O2 -fopenmp -lm runlcm.cpp src/*.cpp

where -fopenmp is optional, it enables the program to run on multi-procesors.

In Windows, the program can be compiled using Visual C++ compiler, just import the files into a new C++ project, and compile it. You may need to enable OpenMP parallellisation manually, see MSDN website for more information.

See Makefile for more information.

Run

A configuration file is needed to run the program. The configuration file defines the the architecture of the model. An example is provided in "para.cfg". Use the following command to run the program

./runlcm –p prefix –f para.cfg -l run.log –o volt.dat.

The options are

-p prefix       Specify the prefix for all files. If no prefix is specified, 
                the current directory will be used.
-f para.cfg     Specify the parameter configuration file (input)
-l run.log      Specify the log file name (output, will be created or rewritten)
-o volt.dat     Specify the voltage output file name 
                (output, will be created or rewritten).

Analysis

The output file is organised in the following format

1. The first 1024 bytes (i.e., 0 to 1023 byte) store header information. This section is organised as parameter name and value pairs. It may also contain comments started with //.

   These following parameters indicate the structure of the other sections

   ELMT_NUM = 400;        //number of element
   NG_NUM = 14;           //number of neuron group
   NUM_SIZE = 4;          //data type size
   CFG_POS = 1024;        //configure section starting position (start from zero)
   CFG_LEN = 25684;       //configure section length
   DATA_POS = 26708;      //data section starting position
   DATA_LEN = 229427200;  //data section length
   BLOCK_SIZE = 22405;    //the size of a block size (voltage information at a time point)
   BLOCK_NUM = 10240;     //number of block in data section
   

2. The parameter configuration information is kept from CFG_POS to CFG_POS+CFG_LEN-1. These are pure text information. The parameter values should be the same as these in the input parameter file, but it also contains additional information about the model, which is generated by the program.

3. The neuronal voltage info is stored from DATA_POS to DATA_POS+DATA_LEN-1.

   They are divided into BLOCK_NUM blocks. Each block stores neuronal voltage information at a time point. The data are stored in binary format using 4-byte floating type (i.e., float type in C and C++), and organised in the following order

   neuron 1 in column 1, neuron 2 in column 1, neuron 3 in column 1, ...
   neuron 1 in column 2, neuron 2 in column 2, neuron 3 in column 2, ...
   

   The order of the neuron groups is the same as their order in the parameter "NEURONS", e.g., NEURONS={neuron_A, neuron_B, ..., neuron_C};.

   The order of the columns is assumed to be

   column 1             ->           column n
   column n+1           ->           column 2n
   ... 
   column n*(n-1)       ->           column n*n 
   

4. A program mktree is provided to demonstrate how to read the voltage file and store them in a ROOT file.

   ROOT is free data analysis framework built on C++ from CERN.

   You need both the ROOT library and the LCM source code to compile the program.

   Assuming you have the LCM source code in directory "src" and a working ROOT software installed, then you can compile the program using the following command

   g++ -o mktree mktree.cpp src/*.cpp -O2 $(root-config --cflags --glibs)

   Usage: ./mktree volt.dat volt.root

   where "volt.dat" is the input file, which is the LCM output file, and "volt.root" is the root file to be created. The third argument is optional. If not given, the root file would be the same as the input file with the extension changed to ".root".

5. A matlab program lcm_load.m, which can read the voltage data into Matlab, is also provided.

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Any problems or permission request for the program should be addressed to jiaxin_dot_du_at_outlook_dot_com or jiaxin_dot_du_at_uqconnect_dot_edu_dot_au (replace _dot_ with . and _at_ with @).

The program is provided for the completeness of the foresaid and future publications. Though every effort has been made to assure the program behaves as prescribed, mistakes or "bugs" may persist. It is the responsibility of users to ensure the "correctness" or "fitness" of the program.

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This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; version 3 of the License.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this program; if not, see http://www.gnu.org/licenses/.