From Vincent.J.Kitsmiller.1 at nd.edu Tue Jul 5 16:49:12 2016 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Tue, 5 Jul 2016 16:49:12 -0400 Subject: [Nirfast] create mesh errors Message-ID: I am having trouble generating a cylindrical mesh. In MATLAB R2014b on MAC I get this error[image: Inline image 1] In MATLAB R2012b on PC I get this error [image: Inline image 2] I can however generate a circular mesh without a problem. Thanks. -Vince -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2016-07-05 at 4.45.16 PM.png Type: image/png Size: 156011 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2016-07-05 at 4.45.27 PM.png Type: image/png Size: 67092 bytes Desc: not available URL: From h.dehghani at cs.bham.ac.uk Tue Jul 5 16:58:35 2016 From: h.dehghani at cs.bham.ac.uk (Hamid Dehghani) Date: Tue, 5 Jul 2016 21:58:35 +0100 Subject: [Nirfast] create mesh errors In-Reply-To: References: Message-ID: I think if you open "optimize_mesh_gui.m" by typing edit optimize_mesh_gui.m and look at line 79, you should comment these 5 lines out: %if myflag % set(handles.text4,'String','Optimization is highly recommended for your mesh due to very poor quality elements!'); %else % set(handles.text4,'String',''); %end Hamid On 05/07/2016 21:49, Vincent Kitsmiller wrote: > I am having trouble generating a cylindrical mesh. In MATLAB R2014b on > MAC I get this errorInline image 1 > In MATLAB R2012b on PC I get this error > Inline image 2 > I can however generate a circular mesh without a problem. Thanks. > > -Vince > > > _______________________________________________ > Nirfast mailing list > Nirfast at public.kitware.com > http://public.kitware.com/mailman/listinfo/nirfast -- -------------------------- Hamid Dehghani, PhD, MIPEM School of Computer Science Acting Director, Physical Sciences for Health Doctoral Training Centre University of Birmingham B15 2TT 0121 414 8728 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 67092 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 156011 bytes Desc: not available URL: From h.dehghani at cs.bham.ac.uk Mon Jul 11 04:53:33 2016 From: h.dehghani at cs.bham.ac.uk (Hamid Dehghani) Date: Mon, 11 Jul 2016 09:53:33 +0100 Subject: [Nirfast] create mesh errors In-Reply-To: References: Message-ID: <517328be-37ed-5959-6db1-2d19ccf88b5d@cs.bham.ac.uk> OK, so this is another error due to MATLAB update. The error is coming from the fact that in a textscan, 'BufSize' argument is now redundant. To fix, edit read_nod_elm (line 45) by typing edit read_nod_elm.m and on approximately line 45, replace data = textscan(fid,'%u32 %f %f %f%*[^\n]','bufsize',409500); with data = textscan(fid,'%u32 %f %f %f%*[^\n]'); I have tested this on a Mac, running MATLAB2016 and it fixes the problem. Hamid On 05/07/2016 21:58, Hamid Dehghani wrote: > > I think if you open "optimize_mesh_gui.m" by typing > > edit optimize_mesh_gui.m > > and look at line 79, you should comment these 5 lines out: > > %if myflag > % set(handles.text4,'String','Optimization is highly recommended > for your mesh due to very poor quality elements!'); > %else > % set(handles.text4,'String',''); > %end > > Hamid > > > On 05/07/2016 21:49, Vincent Kitsmiller wrote: >> I am having trouble generating a cylindrical mesh. In MATLAB R2014b >> on MAC I get this errorInline image 1 >> In MATLAB R2012b on PC I get this error >> Inline image 2 >> I can however generate a circular mesh without a problem. Thanks. >> >> -Vince >> >> >> _______________________________________________ >> Nirfast mailing list >> Nirfast at public.kitware.com >> http://public.kitware.com/mailman/listinfo/nirfast > > -- > -------------------------- > Hamid Dehghani, PhD, MIPEM > School of Computer Science > Acting Director, Physical Sciences for Health Doctoral Training Centre > University of Birmingham > B15 2TT > 0121 414 8728 -- -------------------------- Hamid Dehghani, PhD, MIPEM School of Computer Science Acting Director, Physical Sciences for Health Doctoral Training Centre University of Birmingham B15 2TT 0121 414 8728 http://mi-lab.weebly.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 67092 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: image/png Size: 156011 bytes Desc: not available URL: From Vincent.J.Kitsmiller.1 at nd.edu Tue Jul 19 08:44:37 2016 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Tue, 19 Jul 2016 08:44:37 -0400 Subject: [Nirfast] Meshing and Results Message-ID: I am running standard single wavelength simulations at a number of frequencies between 100-500MHz. I then want to use the results to produce mua and mus values (I do this with another MATLAB script). However when I run simulations with high mus (~>1.5) I am getting nonsensical results as like below. [image: Inline image 1] This is in particular with a cylindrical mesh of radius 100mm and height 60mm with node size 2.1mm. My source and detector are are separated by 20mm and placed 1mm under the top surface. I have however seen this issue with other mesh and node sizes as well. Hopefully you could shed light on this issue and perhaps give me some more information on mesh and node sizes in NIRFAST. Thanks. -Vince -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 11950 bytes Desc: not available URL: From Vincent.J.Kitsmiller.1 at nd.edu Tue Jul 19 10:40:38 2016 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Tue, 19 Jul 2016 10:40:38 -0400 Subject: [Nirfast] Meshing and Results Message-ID: This is the response to Hamid's email. For some reason a reply message failed. The x-axis is frequency. I simply am running the standard forward solver at various frequencies and plotting the amplitudes from NIRFAST versus frequency. -Vince -------------- next part -------------- An HTML attachment was scrubbed... URL: From Vincent.J.Kitsmiller.1 at nd.edu Tue Jul 19 11:31:51 2016 From: Vincent.J.Kitsmiller.1 at nd.edu (Vincent Kitsmiller) Date: Tue, 19 Jul 2016 11:31:51 -0400 Subject: [Nirfast] Fwd: Meshing and Results In-Reply-To: References: <5ab8649a-71b4-c0ce-29d2-be933e0ccd3b@cs.bham.ac.uk> Message-ID: ---------- Forwarded message ---------- From: Vincent Kitsmiller Date: Tue, Jul 19, 2016 at 11:22 AM Subject: Re: [Nirfast] Meshing and Results To: Hamid Dehghani I use the script below and simply extract the amplitude and phase data from the produced .paa file also below. clear all clc npts=10; in=(500-100)/npts; for i=0:npts freq=100+i*in; cylinder_data = femdata('cylinder_mua=0.01_mus=1_n=1.33.rpt',freq); freq=num2str(freq); dataname=strcat('cylinder_',freq,'MHz.paa') save_data(cylinder_data,dataname); end [image: Inline image 1] On Tue, Jul 19, 2016 at 11:13 AM, Hamid Dehghani wrote: > Apologies, I mean y-axis? > > How are you pulling amplitudes out of NIRFAST, and can you give me an > example of commands you use to get data (using femdata I assume) > > Hamid > > On 19/07/2016 15:40, Vincent Kitsmiller wrote: > > This is the response to Hamid's email. For some reason a reply message > failed. > > The x-axis is frequency. I simply am running the standard forward solver > at various frequencies and plotting the amplitudes from NIRFAST versus > frequency. > > -Vince > > > _______________________________________________ > Nirfast mailing listNirfast at public.kitware.comhttp://public.kitware.com/mailman/listinfo/nirfast > > > -- > -------------------------- > Hamid Dehghani, PhD, MIPEM > School of Computer Science > Acting Director, Physical Sciences for Health Doctoral Training Centre > University of Birmingham > B15 2TT > 0121 414 8728 http://mi-lab.weebly.com/ > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Capture.PNG Type: image/png Size: 4210 bytes Desc: not available URL: