From emmanuel.cosnard at outlook.fr Mon Mar 11 10:41:35 2019 From: emmanuel.cosnard at outlook.fr (Emmanuel Cosnard) Date: Mon, 11 Mar 2019 14:41:35 +0000 Subject: [Nirfast] .source and .meas files Message-ID: Hello, I would like to know to what correspond the .meas and .source files, and how I could generate this kind of file by myself (without using NIRFAST slicer)? Thank you and regards, Emmanuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuel.cosnard at outlook.fr Tue Mar 19 06:40:31 2019 From: emmanuel.cosnard at outlook.fr (Emmanuel Cosnard) Date: Tue, 19 Mar 2019 10:40:31 +0000 Subject: [Nirfast] Extinction parameters Message-ID: Hello, I would like to know how exactly do we compute the extinction parameters for each wavelength, that are stored in the excoef file? Thank you and regards, Emmanuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.wojtkiewicz at cs.bham.ac.uk Tue Mar 19 07:13:05 2019 From: s.wojtkiewicz at cs.bham.ac.uk (Stanislaw Wojtkiewicz) Date: Tue, 19 Mar 2019 11:13:05 -0000 Subject: [Nirfast] Extinction parameters In-Reply-To: References: Message-ID: <001701d4de44$b980b7b0$2c822710$@cs.bham.ac.uk> Hi Emmanuel NIRFAST values are expressed in ln(10)*mm^-1mM^-1 (mM - milli molar (molar - moles/liter)) for haemoglobins and in mm^-1 for water. Compare with https://omlc.org/spectra/hemoglobin/summary.html It's the same. Also, this website gives you all information needed. Cheers, S. Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 19 March 2019 10:41 To: nirfast at public.kitware.com Subject: [Nirfast] Extinction parameters Hello, I would like to know how exactly do we compute the extinction parameters for each wavelength, that are stored in the excoef file? Thank you and regards, Emmanuel --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuel.cosnard at outlook.fr Tue Mar 19 08:00:16 2019 From: emmanuel.cosnard at outlook.fr (Emmanuel Cosnard) Date: Tue, 19 Mar 2019 12:00:16 +0000 Subject: [Nirfast] Extinction parameters In-Reply-To: <001701d4de44$b980b7b0$2c822710$@cs.bham.ac.uk> References: , <001701d4de44$b980b7b0$2c822710$@cs.bham.ac.uk> Message-ID: Hi Stanislas, Thank you very much for your answer. There is still a fourth column for each line of the .excoef file, and I don't understand to what it corresponds. Do you know what is the last column about, and how I can fill it? Thank you, Emmanuel ________________________________ De : Stanislaw Wojtkiewicz Envoy? : mardi 19 mars 2019 11:13 ? : emmanuel.cosnard at outlook.fr; nirfast at public.kitware.com Objet : RE: [Nirfast] Extinction parameters Hi Emmanuel NIRFAST values are expressed in ln(10)*mm^-1mM^-1 (mM - milli molar (molar - moles/liter)) for haemoglobins and in mm^-1 for water. Compare with https://omlc.org/spectra/hemoglobin/summary.html It?s the same. Also, this website gives you all information needed. Cheers, S. Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 19 March 2019 10:41 To: nirfast at public.kitware.com Subject: [Nirfast] Extinction parameters Hello, I would like to know how exactly do we compute the extinction parameters for each wavelength, that are stored in the excoef file? Thank you and regards, Emmanuel ________________________________ [Avast logo] This email has been checked for viruses by Avast antivirus software. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.wojtkiewicz at cs.bham.ac.uk Tue Mar 19 08:41:39 2019 From: s.wojtkiewicz at cs.bham.ac.uk (Stanislaw Wojtkiewicz) Date: Tue, 19 Mar 2019 12:41:39 -0000 Subject: [Nirfast] Extinction parameters In-Reply-To: References: , <001701d4de44$b980b7b0$2c822710$@cs.bham.ac.uk> Message-ID: <006601d4de51$19759300$4c60b900$@cs.bham.ac.uk> Hi Emmanuel Lipids I believe. It?s all in the file. As in the excoef.txt file: HbO deoxyHb Water Lipids LuTex GdTex 6.0000000e+02 7.3696000e-01 3.3801592e+00 2.3000000e-04 4.6600000e-04 NaN NaN 6.0100000e+02 6.7523960e-01 3.2586989e+00 2.3400000e-04 4.7100000e-04 NaN NaN You don?t need all columns of the excoef.txt. See ?load_mesh.m? on how excoef.txt file is handled. A hint: The excoef.txt file saves any and any number of spectra. I.e. you can use/define your own spectra! Not all spectra from the ?excoef.txt? are used. The ?*.param? file is used to set spectra in use. E.g. ?cylinder_spec.param? sets only haemoglobins and water: spec HbO deoxyHb Water S-Amplitude S-Power 0.01 0.01 0.4 1 1 0.01 0.01 0.4 1 1 0.01 0.01 0.4 1 1 S. Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 19 March 2019 12:00 To: nirfast at public.kitware.com; s.wojtkiewicz at cs.bham.ac.uk Subject: RE: [Nirfast] Extinction parameters Hi Stanislas, Thank you very much for your answer. There is still a fourth column for each line of the .excoef file, and I don't understand to what it corresponds. Do you know what is the last column about, and how I can fill it? Thank you, Emmanuel _____ De : Stanislaw Wojtkiewicz < s.wojtkiewicz at cs.bham.ac.uk> Envoy? : mardi 19 mars 2019 11:13 ? : emmanuel.cosnard at outlook.fr; nirfast at public.kitware.com Objet : RE: [Nirfast] Extinction parameters Hi Emmanuel NIRFAST values are expressed in ln(10)*mm^-1mM^-1 (mM - milli molar (molar - moles/liter)) for haemoglobins and in mm^-1 for water. Compare with https://omlc.org/spectra/hemoglobin/summary.html It?s the same. Also, this website gives you all information needed. Cheers, S. Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr < emmanuel.cosnard at outlook.fr> Sent: 19 March 2019 10:41 To: nirfast at public.kitware.com Subject: [Nirfast] Extinction parameters Hello, I would like to know how exactly do we compute the extinction parameters for each wavelength, that are stored in the excoef file? Thank you and regards, Emmanuel _____ This email has been checked for viruses by Avast antivirus software. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuel.cosnard at outlook.fr Wed Mar 20 05:35:56 2019 From: emmanuel.cosnard at outlook.fr (Emmanuel Cosnard) Date: Wed, 20 Mar 2019 09:35:56 +0000 Subject: [Nirfast] Normalisation of the measurements? Message-ID: Hello, I would like to know if we have to normalise our fluorescence measurements data in a specific way for the "measurements" vector transmitted in the CSCGNW function (function [xFinal varargout] = CSCGNW(jacobianMatrix, measurements, recParam)). How do we take into account the time of exposure? Do the measures have to be between a specific range, or do we have to apply a specific function on it? Thank you and regards, Emmanuel -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.wojtkiewicz at cs.bham.ac.uk Wed Mar 20 06:01:08 2019 From: s.wojtkiewicz at cs.bham.ac.uk (Stanislaw Wojtkiewicz) Date: Wed, 20 Mar 2019 10:01:08 -0000 Subject: [Nirfast] Normalisation of the measurements? In-Reply-To: References: Message-ID: <001101d4df03$d7732310$86596930$@cs.bham.ac.uk> Hi Emmanuel It looks like the 'CSCGNW' function does not exist in NIRFAST. Even Google knows nothing about it:) Please, track down to whom this function belongs to. Also, regardless of the existence of the function, I have a strong impression that the current question might be outside of the scope of this mailing list.. Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 20 March 2019 09:36 To: nirfast at public.kitware.com Subject: [Nirfast] Normalisation of the measurements? Hello, I would like to know if we have to normalise our fluorescence measurements data in a specific way for the "measurements" vector transmitted in the CSCGNW function (function [xFinal varargout] = CSCGNW(jacobianMatrix, measurements, recParam)). How do we take into account the time of exposure? Do the measures have to be between a specific range, or do we have to apply a specific function on it? Thank you and regards, Emmanuel --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus -------------- next part -------------- An HTML attachment was scrubbed... URL: From emmanuel.cosnard at outlook.fr Wed Mar 20 06:10:48 2019 From: emmanuel.cosnard at outlook.fr (Emmanuel Cosnard) Date: Wed, 20 Mar 2019 10:10:48 +0000 Subject: [Nirfast] Normalisation of the measurements? In-Reply-To: <001101d4df03$d7732310$86596930$@cs.bham.ac.uk> References: , <001101d4df03$d7732310$86596930$@cs.bham.ac.uk> Message-ID: Hello Stanislas, Thank you for taking the time to answer and sorry for my mistake, I am using CSCGNW bioluminescence, and the field I am referring to in NIRFAST is actually data_fn in the reconstruct_fl function. function [fwd_mesh,pj_error] = reconstruct_fl(fwd_mesh,... recon_basis,... frequency,... data_fn,... iteration,... lambda,... output_fn,... filter_n) data_fn are the boundery data measured, and I wanted to know if we have to normalise these data in a specific way. Thank you and regards, Emmanuel ________________________________ De : Stanislaw Wojtkiewicz Envoy? : mercredi 20 mars 2019 10:01 ? : emmanuel.cosnard at outlook.fr; nirfast at public.kitware.com Objet : RE: [Nirfast] Normalisation of the measurements? Hi Emmanuel It looks like the ?CSCGNW? function does not exist in NIRFAST. Even Google knows nothing about it:) Please, track down to whom this function belongs to. Also, regardless of the existence of the function, I have a strong impression that the current question might be outside of the scope of this mailing list?. Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 20 March 2019 09:36 To: nirfast at public.kitware.com Subject: [Nirfast] Normalisation of the measurements? Hello, I would like to know if we have to normalise our fluorescence measurements data in a specific way for the "measurements" vector transmitted in the CSCGNW function (function [xFinal varargout] = CSCGNW(jacobianMatrix, measurements, recParam)). How do we take into account the time of exposure? Do the measures have to be between a specific range, or do we have to apply a specific function on it? Thank you and regards, Emmanuel ________________________________ [Avast logo] This email has been checked for viruses by Avast antivirus software. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From s.wojtkiewicz at cs.bham.ac.uk Wed Mar 20 08:43:21 2019 From: s.wojtkiewicz at cs.bham.ac.uk (Stanislaw Wojtkiewicz) Date: Wed, 20 Mar 2019 12:43:21 -0000 Subject: [Nirfast] Normalisation of the measurements? In-Reply-To: References: , <001101d4df03$d7732310$86596930$@cs.bham.ac.uk> Message-ID: <001301d4df1a$80876e50$81964af0$@cs.bham.ac.uk> Hi Emmanuel Calibrate your data on phantom to express it in photon fluence rate (photons * mm^-2 * s^2) or use differential data. Please refer to vast literature on tomographic reconstruction and perturbation theory. Bioluminescence or NIRS, it does not matter, as the mechanism is all the same. A good start would be: #1 Durduran 2010, Diffuse optics for tissue monitoring and tomography #2 Dehghani 2008, Near infrared optical tomography using NIRFAST: Algorithm for numerical model and image reconstruction Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 20 March 2019 10:11 To: nirfast at public.kitware.com; s.wojtkiewicz at cs.bham.ac.uk Subject: RE: [Nirfast] Normalisation of the measurements? Hello Stanislas, Thank you for taking the time to answer and sorry for my mistake, I am using CSCGNW bioluminescence, and the field I am referring to in NIRFAST is actually data_fn in the reconstruct_fl function. function [fwd_mesh,pj_error] = reconstruct_fl(fwd_mesh,... recon_basis,... frequency,... data_fn,... iteration,... lambda,... output_fn,... filter_n) data_fn are the boundery data measured, and I wanted to know if we have to normalise these data in a specific way. Thank you and regards, Emmanuel _____ De : Stanislaw Wojtkiewicz Envoy? : mercredi 20 mars 2019 10:01 ? : emmanuel.cosnard at outlook.fr; nirfast at public.kitware.com Objet : RE: [Nirfast] Normalisation of the measurements? Hi Emmanuel It looks like the ?CSCGNW? function does not exist in NIRFAST. Even Google knows nothing about it:) Please, track down to whom this function belongs to. Also, regardless of the existence of the function, I have a strong impression that the current question might be outside of the scope of this mailing list . Regards Stanislaw Wojtkiewicz, PhD --- School of Computer Science University of Birmingham B15 2TT From: emmanuel.cosnard at outlook.fr Sent: 20 March 2019 09:36 To: nirfast at public.kitware.com Subject: [Nirfast] Normalisation of the measurements? Hello, I would like to know if we have to normalise our fluorescence measurements data in a specific way for the "measurements" vector transmitted in the CSCGNW function (function [xFinal varargout] = CSCGNW(jacobianMatrix, measurements, recParam)). How do we take into account the time of exposure? Do the measures have to be between a specific range, or do we have to apply a specific function on it? Thank you and regards, Emmanuel _____ This email has been checked for viruses by Avast antivirus software. www.avast.com -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ~WRD000.jpg Type: image/jpeg Size: 823 bytes Desc: not available URL: From emmanuel.cosnard at outlook.fr Fri Mar 29 09:02:00 2019 From: emmanuel.cosnard at outlook.fr (Emmanuel Cosnard) Date: Fri, 29 Mar 2019 13:02:00 +0000 Subject: [Nirfast] Optical properties of a mouse Message-ID: Hello, I am using NIRFAST to perform bioluminescence and fluorescence tomography on small animals. I am really glab to have access to such a great libraryto perform my research. I would like to know if someone had already done that and if he knew the optical properties (?a and ?s') for each organ at several wavelengths, and if to start my research, I could make the approximation that the optical properties of a mouse is homogeneous in its entire body, that is to say if there are some general ?a and ?s' I could use for the entire mouse. Thank you and regards, Emmanuel -------------- next part -------------- An HTML attachment was scrubbed... URL: