From Vincent.J.Kitsmiller.1 at nd.edu Tue Mar 21 12:21:39 2017 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Tue, 21 Mar 2017 12:21:39 -0400 Subject: [Nirfast] excoef.txt Message-ID: What are LuTex and GdTex in the extinction coefficients file? -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2017-03-21 at 12.21.01 PM.png Type: image/png Size: 32973 bytes Desc: not available URL: From Vincent.J.Kitsmiller.1 at nd.edu Wed Mar 22 13:21:06 2017 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Wed, 22 Mar 2017 13:21:06 -0400 Subject: [Nirfast] reconstruction Message-ID: When attempting to run a spectral reconstruction on my own mesh I get the error below. I can however run a reconstruction using the spectral example from the NIRFAST web page. Moving Sources Moving Detectors Moving Sources Moving Detectors Loading data and wavelength information Loading recon basis Creating coarse mesh Coarse mesh created with 900 nodes --------------------------------- Building Jacobian using jacobian_spectral Calculating Jacobian for 650nm Calculating Jacobian for 680nm Calculating Jacobian for 740nm Calculating Jacobian for 770nm Calculating Jacobian for 800nm Calculating Jacobian for 830nm Calculating Jacobian for 860nm Calculating Jacobian for 890nm Calculating Jacobian for 940nm Calculating Jacobian for 950nm Calculating Jacobian for 980nm Subscripted assignment dimension mismatch. Error in jacobian_spectral (line 133) data.paa(:,i*2-1:i*2) = data_tmp(i).paa; Error in reconstruct_spectral_spatial (line 217) [J,data,fwd_mesh] = jacobian_spectral(fwd_mesh,frequency,wv_array,recon_mesh); Error in gui_reconstruct>done_Callback (line 646) evalin('base',content{end}); Error in gui_mainfcn (line 95) feval(varargin{:}); Error in gui_reconstruct (line 42) gui_mainfcn(gui_State, varargin{:}); Error in @(hObject,eventdata)gui_reconstruct('done_Callback',hObject,eventdata,guidata(hObject)) Error while evaluating UIControl Callback From Scott.C.Davis at dartmouth.edu Wed Mar 22 13:29:34 2017 From: Scott.C.Davis at dartmouth.edu (Scott C. Davis) Date: Wed, 22 Mar 2017 17:29:34 +0000 Subject: [Nirfast] excoef.txt In-Reply-To: References: Message-ID: LuTex is Lutetium Texaphyrin and GdTex is Gadolinium Texaphyrin. These are fluorophors/photosensitizers we experimented with many years ago (in fact, we used LuTex in the phantoms reported in our 2007 Optics Express paper showing image-guided FMT). NIRFAST is designed such that you can add as many absorbers as you wish to the excoef file and choose which ones to implement when you run forward/inverse problems. On 3/21/17, 12:21 PM, "Nirfast on behalf of Vincent Kitsmiller" wrote: What are LuTex and GdTex in the extinction coefficients file? From Vincent.J.Kitsmiller.1 at nd.edu Wed Mar 22 14:52:23 2017 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Wed, 22 Mar 2017 14:52:23 -0400 Subject: [Nirfast] reconstruction In-Reply-To: References: Message-ID: when i try running using the "working" script I get a different error... script: clear all % In this example, we will use a 2D case to demonstrate how we can generate % simulated forward data, and use tomographic recontruction from these data % to recover location of anamalies %% Load the 2D multiwavelength wavelength mesh % This mesh is 43 mm in diameter and has 16 source/detectors on the % periphery % The wavelengths being modelled are 661 735 761 785 808 826 % 849 nm mesh_anom = load_mesh('dot_mesh_anom_5mm_deep.rpt'); % Set anomaly size and properties % Anomaly 1 % blob.x=0; % x location % blob.y=15; % y location % blob.r=5; % radius (mm) % blob.region=2; % blob.sa=0.5; % blob.sp=1; % blob.HbO=1; % blob.deoxyHb=0; % blob.Water=0; % blob.Lipids=0; % mesh_anom = add_blob(mesh,blob); % And view the mesh plotmesh(mesh_anom,1); %% Generate forward data using Frequency Domain model at 100 MHz data_anom = femdata(mesh_anom,100); % and add random noise (1% amplitude, and 2 degrees in Phase) data_anom_noise = add_noise(data_anom,1,2); % and view data %plot_data(data_anom_noise); %% Reconstruct lambda.type='Automatic'; lambda.value=1; [mesh_recon,pj] = reconstruct(mesh,[30 30],100,data_anom_noise,40,lambda,'test',0,[650 680 740 770 800 830 860 890 940 950 980]); plotmesh(mesh_recon); % %% Reconstruct assumin some information about location % % in this case, we assume we know the region of the blobs and will use this % % as priori knowledge % % Copy region label into mesh for reconstructing % mesh.region = mesh_anom.region; % lambda=1; % [mesh_recon_spatial,pj] = reconstruct_spectral_spatial(mesh,[30 30],100,data_anom_noise,40,lambda,'spectral_spatial_example',0); % plotmesh(mesh_recon_spatial); error: >> add_blob_fandr_sim Moving Sources Moving Detectors Calculating data for: 650 nm Calculating data for: 680 nm Calculating data for: 740 nm Calculating data for: 770 nm Calculating data for: 800 nm Calculating data for: 830 nm Calculating data for: 860 nm Calculating data for: 890 nm Calculating data for: 940 nm Calculating data for: 950 nm Calculating data for: 980 nm Error using mesh (line 58) Not enough input arguments. Error in add_blob_fandr_sim (line 37) [mesh_recon,pj] = reconstruct(mesh,[30 30],100,data_anom_noise,40,lambda,'test',0,[650 680 740 770 800 830 860 890 940 950 980]); On Wed, Mar 22, 2017 at 1:21 PM, Vincent Kitsmiller wrote: > When attempting to run a spectral reconstruction on my own mesh I get > the error below. I can however run a reconstruction using the spectral > example from the NIRFAST web page. > > Moving Sources > Moving Detectors > Moving Sources > Moving Detectors > Loading data and wavelength information > Loading recon basis > Creating coarse mesh > Coarse mesh created with 900 nodes > --------------------------------- > Building Jacobian using jacobian_spectral > Calculating Jacobian for 650nm > Calculating Jacobian for 680nm > Calculating Jacobian for 740nm > Calculating Jacobian for 770nm > Calculating Jacobian for 800nm > Calculating Jacobian for 830nm > Calculating Jacobian for 860nm > Calculating Jacobian for 890nm > Calculating Jacobian for 940nm > Calculating Jacobian for 950nm > Calculating Jacobian for 980nm > Subscripted assignment dimension mismatch. > > Error in jacobian_spectral (line 133) > data.paa(:,i*2-1:i*2) = data_tmp(i).paa; > > Error in reconstruct_spectral_spatial (line 217) > [J,data,fwd_mesh] = > jacobian_spectral(fwd_mesh,frequency,wv_array,recon_mesh); > > > Error in gui_reconstruct>done_Callback (line 646) > evalin('base',content{end}); > > Error in gui_mainfcn (line 95) > feval(varargin{:}); > > Error in gui_reconstruct (line 42) > gui_mainfcn(gui_State, varargin{:}); > > Error in > @(hObject,eventdata)gui_reconstruct('done_Callback',hObject,eventdata,guidata(hObject)) > > > Error while evaluating UIControl Callback