[Homer-users] re: using homer to generate organ-specific forwardsimulation

[thuppert]

HOMeR supports image reconstructions from semi-infinite, homogeneous, slab
geometries.  The image recontrustion and forward modeling is done through
the PMI toolbox (also avaliable on our website:
http://www.nmr.mgh.harvard.edu/DOT/resources.htm)
For this simple medium, the analytical solution to the forward problem can
be directly computed.  For anything more complicated, we'd have to use monte
carlo or finite difference approaches.  In other words, HOMeR does not
support the realistic head simulations.

For this problem, there are several MC or FD codes avalaible (TOAST from UCL
etc).

>From our lab, we have a MC code avaliable:

tMCimg-  http://www.nmr.mgh.harvard.edu/DOT/resources.htm
	This uses Monte Carlo with arbitary boundaries.



Ted Huppert, M.Sc.

PhD student-Harvard Univ.
Dept of Biophysics
Photon Migration Imaging lab
Mass General Hospital/CNY

Tele: (617)726-1223
Cell: (617) 869-1205

thuppert at nmr.mgh.harvard.edu






-----Original Message-----
From: mrcheung at mdanderson.org [mailto:mrcheung at mdanderson.org]
Sent: Saturday, November 19, 2005 12:13 PM
To: thuppert at nmr.mgh.harvard.edu
Cc: homer-users at nmr.mgh.harvard.edu
Subject: RE: [Homer-users] re: using homer to generate organ-specific
forwardsimulation



Hi Ted,
So can I use homer to generate forward simulation with one source one
detector in reflectance using a realistic head geometry?

If so, pls give me a few pointers on how to do that.

Thx, Rex




      To:   <homer-users at nmr.mgh.harvard.edu>, <mrcheung at mdanderson.org>
      cc:
      bcc:
      Subject:    RE: [Homer-users] re: using homer to generate
organ-specific forwardsimulation
"thuppert" <thuppert at nmr.mgh.harvard.edu>

11/10/2005 11:13 AM EST
Please respond to thuppert          <font size=-1></font>



































No, Homer is actually only used for analysis of functional NIRS data.  Its
particularly designed for functional brain studies.  The image
reconstruction tools in Homer very basic reflecting only those typically
used for such neuroimaging.


We have a number of other resources on our website
(http://www.nmr.mgh.harvard.edu/DOT/resources.htm) which would be of more
use.  The Monte Carlo program tMCimg can allow the calculation of the NIRS
forward problem from heterogenous media

However, there are quite a few other groups that have published on finite
element and MC methods to simulate light propagation which can be used for
your purpose.  In particular, the TOAST program
(http://www.medphys.ucl.ac.uk/%7Emartins/toast/index.html) developed by the
UCL group (http://www.medphys.ucl.ac.uk/research/borg/) can allow mesh
generation and forward solutions.  This is avlaible on their website.



Ted Huppert, M.Sc.

PhD student-Harvard Univ.
Dept of Biophysics
Photon Migration Imaging lab
Mass General Hospital/CNY

Tele: (617)726-1223
Cell: (617) 869-1205

thuppert at nmr.mgh.harvard.edu






-----Original Message-----
From: homer-users-bounces at nmr.mgh.harvard.edu
[mailto:homer-users-bounces at nmr.mgh.harvard.edu]On Behalf Of
mrcheung at mdanderson.org
Sent: Thursday, November 10, 2005 10:46 AM
To: homer-users at nmr.mgh.harvard.edu
Subject: [Homer-users] re: using homer to generate organ-specific
forwardsimulation


I would like to generate a mesh of an organ and put an light source within
the organ and one detector on the surface to collect the light. Is there a
way to simulate this in Homer ?

Thanks, Rex


Assistant Professor,
Department of Radiation Oncology
UT MD Anderson Cancer Center


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