This repository contains the C++ source code used to perform spring registration of a flattened cortical surface to an ideal 2D model in Benson, Butt, Brainard, Aguirre (2014).
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jobs Added the jobs and results directories, as examples. Jan 3, 2014
results Added the jobs and results directories, as examples. Jan 3, 2014
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LICENSE Initial commit Jan 3, 2014
README.md Fixed ROOT and JOB strings in the README.md file. Jan 4, 2014

README.md

SpringRegister

Authors

Primary Author: Noah C. Benson

Principle Investigator: Geoffrey K. Aguirre

Website

The Aguirre lab website contains further information concerning this project.

Citation

This repository is part of the paper: Benson NC, Butt OH, Brainard DH, Aguirre GK (2014) Correction of distortion in flattened representations of the cortical surface allows prediction of V1-V3 functional organization from anatomy. PLoS Comput Biol. Submitted.

Description

This repository contains the C++ source code used to perform spring registration of a flattened cortical surface to an ideal 2D model in Benson, Butt, Brainard, Aguirre (2014).

This src directory contains the source code as well as a Makefile, which will build the springs executable file. This program is designed to compile and run on unix-like systems, and was tested on Mac OS X and Ubuntu. GNU Make version 3.81 and G++ (GCC) version 4.2.1 were used in building the executable. The standard math library (-lm) and POSIX (-lpthread) are also required for building.

This program is intended for use in conjunction with the jobs written by the supplementary Mathematica notebook included in the publication cited above. The springs program is, in fact, a low-level program designed to increase speed and parallelization of the numerical integration used to simulate and minimize the spring system described in Benson et al.

Many command line options to the springs program exist; these can be examined by calling springs -h or springs --help. If you are running simulations whose jobs were exported by the Mathematica notebook, then these options will be specified for you, and you may simply execute the run.sh file that is written. Note that this script expects a certain directory structure in which ROOT/jobs/JOB/run.sh is called from ROOT and in which ROOT/src contains the springs executable. This repository exemplifies this organization (i.e., this repository is a valid replacement for ROOT), and the jobs and results directories analyzed in Benson et al. are included.

License

See LICENSE file.