COBRA is a free set of Matlab functions to segment early visual areas
(Cortical Organization and Border Reconstruction of Retinotopic Areas).
A volumetric phase-encoded retinotopic mapping technique is used to
identify the visual field sign (VFS) of each voxel without the need for
an explicit reconstruction of the cortical surface. The surface-normals
are taken directly from the anatomical MRI. Hereby early visual areas
can be segmented (V1 up to V3A and hV4).
Reference
Dumoulin SO, Hoge RD, Baker Jr CL, Hess RF, Achtman RL,
Evans AC (2003) Automatic volumetric segmentation of human visual
retinotopic cortex. NeuroImage. 18(3): 576-587.
[pdf]
Requirements
In principle COBRA "should" run on all platforms running Matlab, but has only been tested on mips-sgi-irix6.5, alpha-dec-osf4.0, i386-pc-linux-gnu, and ppc-mac-osx3.3 using Matlab 5.3, 6.1 and 6.5.
COBRA requires:
Matlab
: the environment COBRA runs in (5.3 and up),
MINC
: the medical imaging file format COBRA uses (input and output),
EMMA
: a Matlab interface for MINC files,
MNI_AUTOREG
: An automated linear registration package, some of whose functions COBRA uses.
For other BIC tools and information see:
Brain Imaging Software Toolbox,
wiki, or go directly to their
packages-site.
Download
You can download the lastest version here: [cobra_v031.tar.gz].
Good luck! For further information, questions, requests, comments or improvements you can write to me, Serge Dumoulin.
Also, you may want to look at an example and a list of Frequently Asked Questions that I am developing. Older versions and a history of changes can be found here.
Copyright
Copyright © 1998-2004 Serge O. Dumoulin and Richard D. Hoge.
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version as published by the Free Software Foundation.
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.
Acknowledgments
The development of this package was supported by Natural Sciences and Engineering Research Council of Canada (NSERC) Grant OGP0001978 to Curtis Baker, Canadian Institutes of Health Research (CIHR) Grant MT 10818 and MST 34695, and NSERC Grant 0GP0046528 to Robert Hess, and International Consortium for Brain Mapping (ICBM) Grant MH52176-06 to Alan Evans.