[Homer-users] Re: running configure on tMCimg on Linux Fedora
Heval Benav
benav at nmr.mgh.harvard.edu
Tue Nov 22 11:14:51 EST 2005
Hello,
In a Linux shell the current working directory is usually not included in
the PATH, therefore one has to type ./configure , then is should run. You
might experience problems if you have the most current version of "Bison"
installed, you might want to downgrade to Bison 1.8, which worked for me,
or you can try to change libmcparse/parser.y , but this did not work for
me.
Heval
On Tue, November 22, 2005 9:49 am, mrcheung at mdanderson.org said:
>
> 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
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>
> End of Homer-users Digest, Vol 9, Issue 4
> *****************************************
>
>
>
>
>
> _______________________________________________
> Homer-users mailing list
> Homer-users at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/homer-users
>
>
>
---------------------------------------------------------------
Heval Benav eMail: benav at nmr.mgh.harvard.edu
Massachusetts General Hospital
Athinoula A. Martinos Center for Biomedical Imaging
Bldg. 149, 13th Street Charlestown, MA 02129 USA
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