File	Date	Author	Commit
README.txt	2014-10-01	Jonas Richiardi	[78f472] fixed acknowledgements in README main code
_example_use.m	2014-09-29	Jonas Richiardi	[fcd4d7] fixed wrong file for _example_use.m
annotatedStructTemplate116codeBook.mat	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
cylinder2P.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
flexbgv.m	2014-10-01	Jonas Richiardi	[78f472] fixed acknowledgements in README main code
fread3.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
freezeColors.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
jUpperTriMatToVec.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
process_options.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
read_surf.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1
show_FSmesh_export.m	2014-09-20	Jonas Richiardi	[2b523c] Initial commit, with flexbgv version 3.3.1

Read Me

README for flexbgv

WHAT IS THIS?
This is a work-in-progress 3D visualisation package for brain
connectivity graphs, with many neat flexible options. 

It was written by Jonas Richiardi, with numerous contributions
by Nora Leonardi, based on initial code by Dimitri Van De Ville at the
Medical Image Processing Laboratory at EPFL (miplab.epfl.ch), and
benefitted from mesh expertise by Markus Gschwind.

REQUIREMENTS
- To plot a 3D brain mesh (option 'bmesh_show'),
you need to have FreeSurfer installed (http://surfer.nmr.mgh.harvard.edu/).

You can also copy lh.white and rh.white meshes from an existing installation
and set the path in show_FSmesh_export.m. You also need read_surf.m and
fread3.m from  Freesurfer. This is explained in the INSTALLING section below.

INSTALLING
- If you want to display a 3D brain mesh you need to edit show_FSmesh_export.m
and set the variable FSROOTPATH to the root of your FreeSurfer installation.
This code uses brain meshes and read_surf.m and fread3.m from Freesurfer.

STARTING
Look at the _example_use.m script as a starting point, this should give you
results quite quickly.

the main scripts is flexbgv.m

set pp.bmesh_show to true to show brain meshes. See REQUIREMENTS above.

SUPPORT
Ask Jonas Richiardi (richiard@stanford.edu) in case of problems.

REFERENCE
If you use this code please consider citing
Richiardi et al., Classifying minimally disabled multiple sclerosis
patients from resting state functional connectivity, NeuroImage 2012

<http://www.ncbi.nlm.nih.gov/pubmed/22677149>

ACKNOWLEDGEMENTS
The code depends on several external functions (included in the release)
- cylinder2P from Luigi Barone and Per Sundqvist (FEX #5468)
- fread3 and read_surf from the Laboratory for Computational Neuroimaging
  at the Massachusetts General Hospital/Harvard-MIT Health Sciences and
 Technology's Athinoula A. Martinos Center for Biomedical Imaging
 (http://freesurfer.net/) (used to display meshes)
- freezeColors from John Iversen  (FEX #7943)
- process_options from Mark A. Paskin (originally in GraphViz I believe)