[Homer-users] Re: running configure on tMCimg on Linux Fedora
mrcheung at mdanderson.org
mrcheung at mdanderson.org
Tue Nov 22 09:49:58 EST 2005
I downloaded tMCimg. In bash shell, I typed "configure". I got
bash: configure: command not found
What else do I need to do to run configure?
Thx, Rex
homer-users-request at nmr.mgh.ha
rvard.edu To:
Sent by: homer-users at nmr.mgh.harvard.edu
homer-users-bounces at nmr.mgh.ha cc:
rvard.edu
11/21/2005 11:00 AM
Please respond to homer-users
Subject:
Homer-users Digest, Vol 9, Issue 4
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Today's Topics:
1. RE: re: using homer to generate organ-specific
forwardsimulation (thuppert)
2. RE: re: using homer to generate organ-specific
forwardsimulation (mrcheung at mdanderson.org)
----------------------------------------------------------------------
Message: 1
Date: Mon, 21 Nov 2005 09:40:43 -0500
From: "thuppert" <thuppert at nmr.mgh.harvard.edu>
Subject: RE: [Homer-users] re: using homer to generate organ-specific
forwardsimulation
To: <mrcheung at mdanderson.org>
Cc: homer-users at nmr.mgh.harvard.edu
Message-ID:
<MPEJJFJNGIINCGLDHEIAEEDFCJAA.thuppert at nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
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
_______________________________________________
Homer-users mailing list
Homer-users at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
------------------------------
Message: 2
Date: Mon, 21 Nov 2005 10:11:44 -0600
From: mrcheung at mdanderson.org
Subject: RE: [Homer-users] re: using homer to generate organ-specific
forwardsimulation
To: <thuppert at nmr.mgh.harvard.edu>
Cc: homer-users at nmr.mgh.harvard.edu
Message-ID:
<OFABD696AC.E5B7676A-ON862570C0.00587626-862570C0.00593CB3 at mdacc.tmc.edu>
Content-Type: text/plain; charset=iso-8859-1
I downloaded the MC codes from the link below. I have Visual Studio.Net 7.
The workspace provided is for VC++6. Visual Studio.Net 7 updated several
files from the download.
tMCimg.c compiled fine on VS.NET 7. But when I tried to build, I got this
error log. Any suggestions ? Thx, Rex
|---+-------------------------------------------------------------------------------------------------------->
| |
|
|---+-------------------------------------------------------------------------------------------------------->
>
--------------------------------------------------------------------------------------------------------|
|
|
>
--------------------------------------------------------------------------------------------------------|
Build Log
------- Build started: Project: tMCimg, Configuration: Release|Win32
-------
Command Lines
Creating temporary file "c:\optics
codes\tMCimg\tMCimg\tMCimg\Release\RSP000003.rsp" with contents
[
/OUT:".\Release/tMCimg.exe" /INCREMENTAL:NO /NOLOGO /PDB:".
\Release/tMCimg.pdb" /SUBSYSTEM:CONSOLE /MACHINE:X86
kernel32.lib user32.lib gdi32.lib winspool.lib comdlg32.lib
advapi32.lib shell32.lib ole32.lib oleaut32.lib
uuid.lib odbc32.lib odbccp32.lib "\optics
codes\tMCimg\tMCimg\libmcparse\Release\libmcparse.lib" "\optics
codes\tMCimg\tMCimg\libmccore\Release\libmccore.lib"
".\Release\commonMC.obj"
".\Release\erf.obj"
".\Release\tMCimg.obj"
]
Creating command line "link.exe @"c:\optics
codes\tMCimg\tMCimg\tMCimg\Release\RSP000003.rsp""
Output Window
Linking...
LINK : fatal error LNK1181: cannot open input file '\optics
codes\tMCimg\tMCimg\libmcparse\Release\libmcparse.lib'
Results
Build log was saved at "file://c:\optics
codes\tMCimg\tMCimg\tMCimg\Release\BuildLog.htm"
tMCimg - 1 error(s), 0 warning(s)
"thuppert"
<thuppert at nmr.mgh.harvard.edu> To:
<mrcheung at mdanderson.org>
cc:
<homer-users at nmr.mgh.harvard.edu>
11/21/2005 08:40 AM
Please respond to thuppert
Subject:
RE:
[Homer-users] re: using homer to generate organ-specific
forwardsimulation
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
_______________________________________________
Homer-users mailing list
Homer-users at nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
------------------------------
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Homer-users mailing list
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