<div dir="ltr">Dear Kastouri,<div><br></div><div>the error might come from an incorrect realignment of the segmented volumes or from a failure to segment the mri into the wished compartments. You could check the mri images by browsing through the slices with ft_sourcplot([],mri).</div><div>If the mri images are of low quality or contain artefacts, due to set-up devices such as scaffoldings, or ROI boxed images (limiting the volume of acquisition) you are in trouble.</div><div>If you pass the previous check, try again to plot the tessellated surfaces in the same image. Have you done that yet?</div><div><br></div><div>Best</div><div>Cris</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jun 1, 2017 at 8:27 AM, Kasturi Barik <span dir="ltr"><<a href="mailto:kash.kgp@gmail.com" target="_blank">kash.kgp@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Dear all,</div><div><br></div><div>As per last suggestion, I again focus on constructing head-model to<span style="font-size:12.8px"> generate a proper forward model for localization purposes. </span></div><div><span style="font-size:12.8px"><br></span></div><div><u>CODE:</u></div><div><br></div><div>%% 1. read the anatomical data with ft_read_mri;</div><div>load('standard_mri.mat'); </div><div>disp(mri)</div><div>save mri mri<br></div><div><br></div><div>%% Align the coordinate system</div><span class=""><div>cfg = [];</div><div>cfg.method = 'interactive';</div></span><div>cfg.coordsys = 'spm';</div><div>cfg.snapshot = 'yes';</div><div>[mri_aligned] = ft_volumerealign(cfg,mri);</div><div>save mri_aligned mri_aligned</div><div><br></div><div>%% 2. SEGMENTATION</div><div>% set path of means go to : D:\MATLAB\toolbox\fieldtrip-<wbr>20140401\external\spm8</div><div>cfg = [];</div><div>cfg.output = {'brain','skull','scalp'};</div><div>segmentedmri = ft_volumesegment(cfg, mri_aligned);</div><div>save segmentedmri segmentedmri</div><div><br></div><div>%% 3. triangulate the surfaces with ft_prepare_mesh;</div><div>cfg = [];</div><div>cfg.tissue = {'brain','skull','scalp'};</div><div>cfg.numvertices = [3000 2000 1000];</div><div>bnd = ft_prepare_mesh(cfg,<wbr>segmentedmri);</div><div>save bnd bnd</div><div><br></div><div>%% 4. Create headmodel</div><div>cfg = [];</div><div>cfg.method = 'bemcp'; % You can also specify 'openmeeg', 'bemcp', or another method.</div><div>% cfg.conductivity = [0.3300 0.0041 0.3300];</div><div>vol1 = ft_prepare_headmodel(cfg, bnd);</div><div><br></div><div><pre style="white-space:pre-wrap"><i style="color:rgb(0,0,0)">When running these settings </i><i style="color:rgb(0,0,0)">I am getting the following error message:</i></pre></div><div><font color="#000000"><div style="font-style:italic">Error using surface_nesting (line 26)</div><div style="font-style:italic">the compartment nesting cannot be determined</div><div style="font-style:italic"><br></div><div style="font-style:italic">Error in ft_headmodel_bemcp (line 66)</div><div style="font-style:italic">order = surface_nesting(vol.bnd, 'insidefirst');</div><div style="font-style:italic"><br></div><div style="font-style:italic">Error in ft_prepare_headmodel (line 257)</div><div style="font-style:italic"> vol = ft_headmodel_bemcp(geometry, 'conductivity',</div><div style="font-style:italic"> cfg.conductivity);</div><div style="font-style:italic"><br></div><div> <span style="font-size:12.8px;white-space:pre-wrap;color:rgb(34,34,34)"><font color="#000000">I am not able to detect, where is the problem. </font></span><span style="font-size:12.8px;white-space:pre-wrap;color:rgb(34,34,34)"><font color="#000000">I would be very thankful if you can help me in this regard. </font></span></div></font></div><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, May 31, 2017 at 5:19 PM, Cristiano Micheli <span dir="ltr"><<a href="mailto:michelic72@gmail.com" target="_blank">michelic72@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div>Dear Kastouri,<br><br></div>My hunch is that either ft_prepare_headmodel or ft_prepare_leadfield fail in generating a proper forward model for localization purposes.<br></div>I would check that ft_prepare_headmodel's vol structure contains sensible data by plotting both the 'bnd' triangulated surface and the EEG electrodes together (you should be able to find instructions on the wiki) in the same image. Sometimes units (mm,cm) or coregistration (left/right swap) might influence a good outcome.<br></div>Accordingly the grid.leadfield structure will not make sense because it uses the incorrect outcome of the vol structure.<br><br></div>So if you manage to solve the 1st problem you'll kill two bird with a stone<br></div>Good luck!<br></div>Cris<br><div><div><div><div><br><br><br><br></div></div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_-8159685233416734036h5">On Wed, May 31, 2017 at 12:50 PM, Kasturi Barik <span dir="ltr"><<a href="mailto:kash.kgp@gmail.com" target="_blank">kash.kgp@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_-8159685233416734036h5"><div dir="ltr"><div class="gmail_quote"><div dir="ltr"><pre style="white-space:pre-wrap"><i style="color:rgb(0,0,0)">Dear all,
</i><i style="color:rgb(0,0,0)">
</i><i style="color:rgb(0,0,0)">I am trying to perform source localization in the frequency domain </i></pre><pre style="white-space:pre-wrap"><i style="color:rgb(0,0,0)">from EEG data using 'DICS' . As I have no mri data of the participants, </i></pre><pre style="white-space:pre-wrap"><i style="color:rgb(0,0,0)">I am using </i><font color="#000000"><i>'Subject01.mri' to read the anatomical data with ft_read_mri. </i></font></pre><pre style="white-space:pre-wrap"><font color="#000000"><i>The </i></font><i>head model created with 'bemcp'.</i></pre><pre style="white-space:pre-wrap"><i style="color:rgb(0,0,0)">Code:</i></pre><pre style="white-space:pre-wrap"><font face="arial, helvetica, sans-serif"><i style="color:rgb(0,0,0)">%% </i><font color="#000000"><i>Read the anatomical data</i></font></font></pre><pre style="white-space:pre-wrap"><i style="font-family:arial,sans-serif"><font color="#000000"><font face="arial, helvetica, sans-serif">mri = ft_read_mri('Subject01.mri');</font></font></i></pre><pre style="white-space:pre-wrap"><font face="arial, helvetica, sans-serif"><i style="color:rgb(0,0,0)">%% </i></font><font face="arial, helvetica, sans-serif" color="#000000"><i>Segment the anatomical information & triangulate the surfaces</i></font></pre><div style="font-size:12.8px"><i><font color="#000000">load segmentedmri % load from </font></i><a href="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/headmodel_eeg/segmentedmri.mat" class="m_-8159685233416734036m_-1409750332907050831m_3169683296666377404m_-8657161844681314279gmail-m_8088325427694831497gmail-urlextern" title="ftp://ftp.fieldtriptoolbox.org/pub/fieldtrip/tutorial/headmodel_eeg/segmentedmri.mat" rel="nofollow" style="color:rgb(51,153,243);box-sizing:border-box;background-color:transparent;outline:0px;background-repeat:no-repeat;background-position:0px 50%;padding:0px 0px 0px 18px;background-image:url("");font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:14px;text-align:justify" target="_blank">ftp server</a><span style="color:rgb(102,102,102);font-family:"Open Sans","Helvetica Neue",Helvetica,Arial,sans-serif;font-size:14px;text-align:justify;background-color:rgb(255,255,204)"> (segmentedmri.mat).</span><i><br></i></div><div style="font-size:12.8px"><i><font color="#000000">load bnd</font></i></div><div style="font-size:12.8px"><i><font color="#000000"><br></font></i></div><div style="font-size:12.8px"><i><font color="#000000">%% </font></i><font color="#000000"><i>Create the headmodel</i></font></div><div style="font-size:12.8px"><i><font color="#000000"><div>cfg = [];</div><div>cfg.method = 'bemcp'; </div><div>vol = ft_prepare_headmodel(cfg, bnd);</div><div><br></div><div>%% Position of the electrodes<br></div><div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><div style="display:inline">load('Face_sub.mat'); % data of participants' electrode positions</div> </div></font></i><br></div><div>electrodes = Face_sub.elec;</div></div><div><br></div><div>%% Interactive alignment<br></div><div><div>cfg = [];</div><div>cfg.method = 'interactive';</div><div>cfg.elec = electrodes;</div><div>cfg.headshape = vol.bnd(3); % scalp</div><div>elec_aligned = ft_electroderealign(cfg);</div><div><br></div><div>%% Compute leadfield:<br></div><div><div>cfg = [];</div><div>cfg.elec = elec_aligned;</div><div>cfg.vol = vol;</div><div>cfg.channel = {'EEG'};</div><div>[grid] = ft_prepare_leadfield(cfg);</div></div></div><div><br></div><div><div>%% Source Analysis</div><div>cfg = []; </div><div>cfg.method = 'dics';</div><div>cfg.frequency = 10; </div><div>cfg.grid = grid;</div><div>cfg.vol = vol;</div><div>cfg.dics.projectnoise = 'yes';</div><div>cfg.dics.lambda = 0;</div><div>sourceFace = ft_sourceanalysis(cfg, face_data); % face_data is obtained from the FT_FREQANALYSIS % <i><font color="#000000"> <div style="display:inline"><div style="display:inline"> </div></div></font></i></div><div><i><font color="#000000"><div style="display:inline"><div style="display:inline"><br></div></div></font></i></div><div><i><font color="#000000"><div style="display:inline"><div style="display:inline">[%% time frequency analysis </div> </div></font></i><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div>| cfg = []; <i style="color:rgb(34,34,34)"><font color="#000000"> <div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div> </font></i> cfg.channel = 'EEG'; <i style="color:rgb(34,34,34)"><font color="#000000"> <div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div> </font></i><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><div style="display:inline"> cfg.method = 'mtmfft'; </div> </div></font></i><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div> </font></i> cfg.output = 'powandcsd'; <i style="color:rgb(34,34,34)"><font color="#000000"> <div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div> </font></i> cfg.tapsmofrq = 4; <i style="color:rgb(34,34,34)"><font color="#000000"> <div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div> </font></i> cfg.foi = 1:1:40; <i style="color:rgb(34,34,34)"><font color="#000000"> <div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div></font></i></div><div><i style="color:rgb(34,34,34)"><font color="#000000"><div style="display:inline"><i style="color:rgb(34,34,34)"><font color="#000000">|</font></i></div> </font></i> face_data = ft_freqanalysis(cfg, Face_sub); ]</div></div></font></i></div><pre style="white-space:pre-wrap"><i style="color:rgb(0,0,0)">When running DICS with these settings </i><i style="color:rgb(0,0,0)">I am getting the following error message:</i></pre><pre style="white-space:pre-wrap"><i><font color="#000000">Error using svd
Input to SVD must not contain NaN or Inf.
Error in beamformer_dics>pinv (line 650)
[U,S,V] = svd(A,0);
Error in beamformer_dics (line 339)
filt = pinv(lf' * invCf * lf) * lf' * invCf;
% Gross eqn. 3, use PINV/SVD to cover rank
deficient leadfield
Error in ft_sourceanalysis (line 568)
dip(i) = beamformer_dics(grid, sens, vol, [],
squeeze(Cf(i,:,:)), optarg{:});
Error in SourceAnalysis (line 133)
sourceFace = ft_sourceanalysis(cfg, face_data);<br></font></i></pre><div style="font-size:12.8px"><br></div><div style="font-size:12.8px"><pre style="white-space:pre-wrap"><i><font color="#000000"> I am not able to detect, where is the problem. Another issue I have found that 'vol.mat' or 'grid.leadfield' are all NaN value. I cannot understand how to solve it. I would be very thankful if you can help me in this regard. </font></i></pre></div><span class="m_-8159685233416734036m_-1409750332907050831HOEnZb"><font color="#888888"><span class="m_-8159685233416734036m_-1409750332907050831m_3169683296666377404HOEnZb"><font color="#888888"><br><div><br></div></font></span></font></span></div></div><span class="m_-8159685233416734036m_-1409750332907050831HOEnZb"><font color="#888888"><br clear="all"><div><br></div>-- <br><div class="m_-8159685233416734036m_-1409750332907050831m_3169683296666377404gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr">Thanks & Regards<div><br></div><div><font color="#0000ff"><b>Kasturi Barik</b></font><br><div><b><br></b></div><div><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">MS Research Scholar</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Audio and Bio-signal Processing Lab</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Department of Electronics and Electrical Engineering</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Indian Institute of Technology Kharagpur</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Mob: <a href="tel:+91%2089024%2000644" value="+918902400644" target="_blank">+91-8902400644</a></span><b><br></b></div></div></div></div></div></div>
</font></span></div>
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<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="m_-8159685233416734036gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr">Thanks & Regards<div><br></div><div><font color="#0000ff"><b>Kasturi Barik</b></font><br><div><b><br></b></div><div><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">MS Research Scholar</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Audio and Bio-signal Processing Lab</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Department of Electronics and Electrical Engineering</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Indian Institute of Technology Kharagpur</span><br style="color:rgb(102,0,204);font-family:tahoma,sans-serif"><span style="color:rgb(102,0,204);font-family:tahoma,sans-serif">Mob: <a href="tel:+91%2089024%2000644" value="+918902400644" target="_blank">+91-8902400644</a></span><b><br></b></div></div></div></div></div></div>
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