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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Hi JM,<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>I would like to let you know that a colleague of mine, Diego Lozano-Soldevilla, figured it out that the issue was that the warping uses “old” spmmethods as defaults. Switching to “new” resulted in a good spatial correspondence between the headmodel and the sourcemodel.<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><p class=MsoNormal>Kind regards,<o:p></o:p></p><p class=MsoNormal><span lang=HU>Tibor <o:p></o:p></span></p><p class=MsoNormal><span lang=HU><o:p> </o:p></span></p><p class=MsoNormal><b><span lang=HU style='color:#222A35'>Auer, Tibor M.D. Ph.D.<o:p></o:p></span></b></p><p class=MsoNormal><a href="mailto:tibor.auer@gmail.com"><span lang=HU style='color:#0563C1'>tibor.auer@gmail.com</span></a><span lang=HU><o:p></o:p></span></p><p class=MsoNormal><span lang=HU style='color:#222A35'>+44-7906-863837<o:p></o:p></span></p><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7C0da68a9196be4a4fd60108d71a70e11e%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637006944417188277&sdata=aoE%2FhNWj%2F%2F3L8fDDz4S0dMuMTlt2p05mgHaDTXddP4w%3D&reserved=0"><span lang=HU style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US>From:</span></b><span lang=EN-US> tibor.auer@gmail.com <tibor.auer@gmail.com> <br><b>Sent:</b> 29 September 2020 11:13<br><b>To:</b> 'FieldTrip discussion list' <fieldtrip@science.ru.nl><br><b>Subject:</b> RE: [FieldTrip] eLORETA source analysis<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>Hi JM,<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>I can confirm that the volumes match:<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>mri = <o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> struct with fields:<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> dim: [176 240 256]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> anatomy: [176×240×256 double]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> hdr: [1×1 struct]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> transform: [4×4 double]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> unit: 'mm'<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> inside: [176×240×256 logical]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> coordsys: 'ras'<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>>> seg<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>seg = <o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> struct with fields:<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> dim: [176 240 256]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> transform: [4×4 double]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> unit: 'mm'<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> coordsys: 'ras'<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> gray: [176×240×256 double]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> white: [176×240×256 double]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> csf: [176×240×256 double]<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>>> V = spm_vol(segfn);<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>>> V(1).mat<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>ans =<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 1.0000 0 0 -92.7090<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 0 1.0000 0 -134.8915<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 0 0 1.0000 -147.5172<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 0 0 0 1.0000<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>>> seg.transform<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>ans =<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 1.0000 0 0 -92.7090<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 0 1.0000 0 -134.8915<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 0 0 1.0000 -147.5172<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'> 0 0 0 1.0000<o:p></o:p></span></i></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><i><span style='mso-fareast-language:EN-US'>seg.transform</span></i><span style='mso-fareast-language:EN-US'> is taken from <i>mri.transform</i>, so they are equivalent.<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'>I have also attached two images showing spatial correspondence of the matrices based on ths code:<o:p></o:p></span></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>%%<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>subplot(1,2,1);<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>imagesc(mri.anatomy(:,:,165)); colormap(gray); axis image<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>subplot(1,2,2);<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>imagesc(seg.gray(:,:,165)>0.99); colormap(gray); axis image<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>%%<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>img = mri.anatomy/max(mri.anatomy(:))*128;<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>c1 = seg.gray.*(seg.gray>0.9)-0.9; c1 = c1.*(c1>0);<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>c1 = (c1/0.1*128+128).*(c1>0);<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>img = img + c1;<o:p></o:p></span></i></p><p class=MsoNormal style='margin-left:35.4pt'><i><span style='mso-fareast-language:EN-US'>image(img(:,:,165)); colormap([gray(128);hot(128)]); axis image<o:p></o:p></span></i></p><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><p class=MsoNormal>Kind regards,<o:p></o:p></p><p class=MsoNormal>Tibor <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow<o:p></o:p></span></b></p><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><span style='color:#0066FF'><o:p></o:p></span></p><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><u><span style='color:#0563C1'><o:p></o:p></span></u></p><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div><p class=MsoNormal><span style='mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b>From:</b> fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>> <b>On Behalf Of </b>Schoffelen, J.M. (Jan Mathijs)<br><b>Sent:</b> Tuesday, September 29, 2020 7:11 AM<br><b>To:</b> FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b> Re: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Tibor, <o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>I don’t know what is wrong with this snippet, apart from the fact that there’s no guarantee that the volume in mri.anatomy matches (in terms of voxel dimensions and orientation) with the volumes that you load in with spm_read_vols.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>JM<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><p class=MsoNormal>On 28 Sep 2020, at 23:00, <a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a> wrote:<o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>Hi JM,<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Can you tell me what is wrong with the snippet below? It generates the attached image (i.e. the headmodel and the sourcemodel do not match).<o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>FTpath = '/users/psychology01/software/fieldtrip';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i> </i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>mrifn = 'T1w.nii';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>mri = ft_read_mri(mrifn,'dataformat','nifti_spm');</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>mri = ft_datatype_volume(mri);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>mri.coordsys = 'ras';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i> </i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>segfn = char('c1.nii','c2.nii','c3.nii');</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>Y = spm_read_vols(spm_vol(segfn));</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>seg = keepfields(mri,{'dim','transform','coordsys','unit'});</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>seg.gray = Y(:,:,:,1);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>seg.white = Y(:,:,:,2);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>seg.csf = Y(:,:,:,3);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>clear Y</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i> </i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg = [];</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg.method = 'singleshell';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>headmodel = ft_prepare_headmodel(cfg, seg);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i> </i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>dat = load(fullfile(FTpath,'template/sourcemodel/standard_sourcemodel3d10mm.mat'));</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg = [];</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg.warpmni = 'yes';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg.template = dat.sourcemodel;</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg.nonlinear = 'yes';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg.mri = mri;</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>cfg.unit ='mm';</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>sourcemodel = ft_prepare_sourcemodel(cfg);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i> </i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>% make a figure of the single subject headmodel, and grid positions</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>figure; hold on;</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>ft_plot_headmodel(headmodel, 'edgecolor', 'none','facecolor',[0.5 0.5 0.5],'facealpha', 0.4);</i><o:p></o:p></p></div><div style='margin-left:35.4pt'><p class=MsoNormal><i>ft_plot_mesh(sourcemodel.pos(sourcemodel.inside,:));</i><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span><<a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a>><span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Monday, September 28, 2020 5:03 PM<br><b>To:</b><span class=apple-converted-space> </span>'FieldTrip discussion list' <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>RE: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>I found it:<span class=apple-converted-space> </span><a href="http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#make-the-individual-subjects-grid">http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#make-the-individual-subjects-grid</a><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span><<a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a>><span class=apple-converted-space> </span><br><b>Sent:</b><span class=apple-converted-space> </span>Monday, September 28, 2020 5:00 PM<br><b>To:</b><span class=apple-converted-space> </span>'FieldTrip discussion list' <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>RE: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>And how do I inverse-warp them?<span class=apple-converted-space> </span><span style='font-family:"Segoe UI Emoji",sans-serif'>😊</span><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Schoffelen, J.M. (Jan Mathijs)<br><b>Sent:</b><span class=apple-converted-space> </span>Monday, September 28, 2020 4:37 PM<br><b>To:</b><span class=apple-converted-space> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal>Dear Tibor,<span class=apple-converted-space> </span><o:p></o:p></p></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Well, I meant you can use one of the standard sourcemodels, provided you inverse-warp them to individual subject space.<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Best wishes,<o:p></o:p></p></div></div><div><div><p class=MsoNormal>Jan-Mathijs<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div><div><p class=MsoNormal style='margin-bottom:12.0pt'> <o:p></o:p></p><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><p class=MsoNormal>On 28 Sep 2020, at 17:25,<span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span>wrote:<o:p></o:p></p></div></div><div><p class=MsoNormal> <o:p></o:p></p></div><div><div><div><p class=MsoNormal>Do you mean I could simply use <fieldtrip>/template/sourcemodel/standard_sourcemodel3d10mm.mat?<o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div></div><div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div></div><div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div></div><div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div></div><div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Schoffelen, J.M. (Jan Mathijs)<br><b>Sent:</b><span class=apple-converted-space> </span>Monday, September 28, 2020 3:28 PM<br><b>To:</b><span class=apple-converted-space> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal>Well, the group analysis section should be sufficient.<span class=apple-converted-space> </span><o:p></o:p></p></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Best wishes,<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>JM<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'> <o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><p class=MsoNormal>On 28 Sep 2020, at 16:20,<span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span>wrote:<o:p></o:p></p></div></div></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><div><div><p class=MsoNormal>Hi JM,<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Thank you for the information.<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Regarding 3D grids, the<span class=apple-converted-space> </span><a href="http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#construction-of-a-source-model-based-on-a-regular-3-dimensional-grid-of-dipole-positions">http://www.fieldtriptoolbox.org/tutorial/sourcemodel/#construction-of-a-source-model-based-on-a-regular-3-dimensional-grid-of-dipole-positions</a><span class=apple-converted-space> </span>section says “Content is coming soon!”. Only the steps required for group analysis are detailed.<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><div><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Schoffelen, J.M. (Jan Mathijs)<br><b>Sent:</b><span class=apple-converted-space> </span>Monday, September 28, 2020 1:05 PM<br><b>To:</b><span class=apple-converted-space> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal>Hi Tibor,<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>Well, I don’t have a strong recommendation to go for either, apart from the fact that a distributed source reconstruction method (such as eLORETA) benefits from an accurate source model to begin with. Also, it depends on what you aim in your source reconstruction. Limiting yourself to the cortical sheet gets rid subcortical structures/cerebellum.<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>Regarding 3D grids, there is some stuff that relates to 3D grids, isn’t there?<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>Best wishes,<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>JM<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br><br><o:p></o:p></p></div></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><div><p class=MsoNormal>On 28 Sep 2020, at 13:52,<span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span>wrote:<o:p></o:p></p></div></div></div></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><div><div><div><div><p class=MsoNormal>Thank you, Jan-Mathijs,<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>This link is very instructive. I wonder why it eluded me so far.<span class=apple-converted-space> </span><span style='font-family:"Segoe UI Emoji",sans-serif'>😊</span><o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>If I get it right, you recommend using approach based on the cortical sheet because 1) the tutorial for 3D grid is not there yet and 2) I can use results from cortical sheet directly for group analysis.<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><div><div><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Schoffelen, J.M. (Jan Mathijs)<br><b>Sent:</b><span class=apple-converted-space> </span>Monday, September 28, 2020 10:21 AM<br><b>To:</b><span class=apple-converted-space> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal>Dear Tibor,<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>It’s not clear to me what’s special about spm’s ‘unified segmentation’ regarding the creation of source models. <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>I assume you are aware that source models eventually need to be in the subject’s native space in order for them to be useable.<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Documentation about how to create a source model for EEG/MEG source reconstruction can be found at: <a href="http://www.fieldtriptoolbox.org/tutorial/sourcemodel/">http://www.fieldtriptoolbox.org/tutorial/sourcemodel/</a>, which might be a good starting point. <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Best wishes,<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Jan-Mathijs<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br><br><br><o:p></o:p></p></div></div></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><div><div><p class=MsoNormal>On 28 Sep 2020, at 10:03,<span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span>wrote:<o:p></o:p></p></div></div></div></div></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Hi Jan-Mathijs,<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Thank you for your response. I found that post earlier and noticed that I may need to redo the freqanalysis, however, I still do not know how do I create the<span class=apple-converted-space> </span><i>sourcemodel</i><span class=apple-converted-space> </span>from the T1-weighted MRI images already segmented with SPM12.<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal><a href="mailto:T.Auer@surrey.ac.uk"><span style='color:#0563C1'>T.Auer@surrey.ac.uk</span></a><o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><div><div><div><div><div><p class=MsoNormal><b>From:</b><span class=apple-converted-space> </span>fieldtrip <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>><span class=apple-converted-space> </span><b>On Behalf Of<span class=apple-converted-space> </span></b>Schoffelen, J.M. (Jan Mathijs)<br><b>Sent:</b><span class=apple-converted-space> </span>Thursday, September 24, 2020 8:12 AM<br><b>To:</b><span class=apple-converted-space> </span>FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br><b>Subject:</b><span class=apple-converted-space> </span>Re: [FieldTrip] eLORETA source analysis<o:p></o:p></p></div></div></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal>Hi Tibor,<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Some of this is discussed (and fixed, there were some small issues in the code) in <a href="https://github.com/fieldtrip/fieldtrip/issues/1454">https://github.com/fieldtrip/fieldtrip/issues/1454</a> and the PR that is linked in the linked issue.<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Note: if you want to go from sensor-level to source-level data in the frequency domain, you should either use ‘powandcsd’, or ‘fourier’ as cfg.output argument to ft_freqanalysis.<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Best wishes,<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Jan-Mathijs<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal style='margin-bottom:12.0pt'><br><br><br><br><o:p></o:p></p></div></div></div></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><div><div><div><div><div><div><p class=MsoNormal>On 23 Sep 2020, at 13:42,<span class=apple-converted-space> </span><a href="mailto:tibor.auer@gmail.com">tibor.auer@gmail.com</a><span class=apple-converted-space> </span>wrote:<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><div><div><div><div><p class=MsoNormal>Dear Community,<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>I would like to perform an eLORETA source analysis, however, I am unsure about the steps.<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>I am working on the<span class=apple-converted-space> </span><a href="http://fcon_1000.projects.nitrc.org/indi/retro/MPI_LEMON.html"><span style='color:#0563C1'>LEMON data</span></a><span class=apple-converted-space> </span>including 62-channel EEG experiment at rest and structural (T1-weighted) MRI of >200 participants.<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>I have preprocessed the EEG data and performed timefrequency analysis on the 2-second-long epochs with configuration:<o:p></o:p></p></div></div></div></div></div></div><ul style='margin-top:0cm' type=disc><ul style='margin-top:0cm' type=circle><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>method: 'mtmfft'<o:p></o:p></li><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>taper: 'hanning'<o:p></o:p></li><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>foi: [0.9766 1.9531 3.9062 5.8594 7.8125 12.2070 15.1367 20.0195 24.9023 32.2266 40.0391 60.0586 69.8242 80.0781 95.2148 109.8633 120.1172]<o:p></o:p></li><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>pad: 2.0480<o:p></o:p></li><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>output: 'pow'<o:p></o:p></li><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>keeptrials: 'no'<o:p></o:p></li><li class=MsoListParagraph style='margin-top:0cm;margin-bottom:0cm;mso-list:l0 level2 lfo3'>trials: [233×1 double]<o:p></o:p></li></ul></ul><div><div><div><div><div><div><p class=MsoNormal>I have also processed the MRI images and normalised-segmented them using SPM12’s unified segmentation outside FieldTrip.<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>I would appreciate any help including code snippets, pointers to (order of) functions or specific and detailed tutorials.<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Kind regards,<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>Tibor<span class=apple-converted-space> </span><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal><b><span style='color:#222A35'>Auer, Tibor M.D. Ph.D.</span></b><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>Research Fellow</span></b><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal><b><span style='color:#0066FF'>School of Psychology, Faculty of Health and Medical Sciences</span></b><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal>University of Surrey, Guildford GU2 7XH<o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal><a href="https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.com%2FTiborAuer&data=02%7C01%7Ct.auer%40surrey.ac.uk%7Cdb32da458c424eedef2908d7d4bd1421%7C6b902693107440aa9e21d89446a2ebb5%7C0%7C0%7C637211780868086968&sdata=zrT5%2FnGGsar14C3WartuU99tzsfLu30Peh9fuaqrAUg%3D&reserved=0"><span style='color:#0563C1'>@TiborAuer</span></a><o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>dy>_______________________________________________<br>fieldtrip mailing list<br></span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#0563C1'>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'><br></span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif;color:#0563C1'>https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p></div></div></div></div></div></div></blockquote></div><div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div></div><div><div><div><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>v>_______________________________________________<br>fieldtrip mailing list<br></span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'><br></span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p></div></div></div></div></div></blockquote></div><div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div></div><div><div><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>_______________________________________________<br>fieldtrip mailing list<br><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip">https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br><a href="https://doi.org/10.1371/journal.pcbi.1002202">https://doi.org/10.1371/journal.pcbi.1002202</a></span><o:p></o:p></p></div></div></div></div></blockquote></div><div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div></div><div><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>div>_______________________________________________<br>fieldtrip mailing list<br></span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'><br></span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p></div></div></div></blockquote></div><div><div><p class=MsoNormal> <o:p></o:p></p></div></div></div><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>/p>_______________________________________________<br>fieldtrip mailing list<br></span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'><br></span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p></div></div></blockquote></div><div><p class=MsoNormal> <o:p></o:p></p></div></div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>nbsp;</span> <o:p></o:p></p><div><p class=MsoNormal><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'><o:p> </o:p></span></p></div><p class=MsoNormal><fieldtrip.png><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>_______________________________________________<br>fieldtrip mailing list<br></span><a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://mailman.science.ru.nl/mailman/listinfo/fieldtrip</span></a><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'><br></span><a href="https://doi.org/10.1371/journal.pcbi.1002202"><span style='font-size:10.5pt;font-family:"Helvetica",sans-serif'>https://doi.org/10.1371/journal.pcbi.1002202</span></a><o:p></o:p></p></div></blockquote></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>