I think the problem is in the first steps, where i used neuromag coordinates... and i have to work in CTF and then to Talairach... i'll try it againg.<br><br><div class="gmail_quote">2012/1/27 Ion Lavado <span dir="ltr"><<a href="mailto:lavado@gmail.com">lavado@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Ok, thank you for your time Arjen. This is what i've done:<br><br><br><br><br><br><b><span style="color:rgb(51,51,255)">%READ AND REALINGN</span></b><br>
mri = ft_read_mri('C:\Users\ilavado\Desktop\31_CW1AFMRI_ESG_ENDIKA_SANCHEZ_GOMEZ\1_028_t1_mpr_tra_p2_iso_20110314\31_CW1AFMRI_ESG_ENDIKA_SANCHEZ_GOMEZ_20110314_001_028_t1_mpr_tra_p2_iso.img');<br>
cfg = [];<br>cfg.interactive = 'yes';<br>cfg.coordsys = 'neuromag';<br>mri_other = ft_volumerealign(cfg,mri); <br><br><b><span style="color:rgb(51,51,255)">%RESLICING</span></b><br>cfg = [];<br>
cfg.resolution=1;<br>cfg.dim=[256 256 256];<br>mrirs = ft_volumereslice(cfg, mri_other);<br>save mrirs;<br><br><b><span style="color:rgb(51,51,255)">%SEGMENTATION</span></b><br>load mrirs;<br>cfg = [];<br>cfg.coordsys = 'neuromag';<br>
cfg.output={'skullstrip' 'brain'};<br>seg = ft_volumesegment(cfg, mrirs)<br>save seg seg;<br><br><b style="color:rgb(51,51,255)">%REALING TO TALAIRACH</b><br>load mrirs;<br>cfg=[];<br>cfg.method='interactive';<br>
cfg.coordsys = 'neuromag';<br>mri_tal=ft_volumerealign(cfg,mrirs); <span style="color:rgb(0,102,0)"> <b>%mrirs o mri_other???</b></span><br>save mri_tal mri_tal<br><br><br>seg.transform = mri_tal.transform;<br>
cfg = [];<br>cfg.filename = 'Subject29_mri_freesurfer2';<br>cfg.filetype = 'mgz';<br>cfg.parameter = 'anatomy';<br>ft_volumewrite(cfg, mri_tal);<br><br>cfg.filename = 'Subject29masked2';<br>
ft_volumewrite(cfg, seg);<br><br><br><br>THE I CREATE ALL THE FILES (WITH THE TUTORIAL COMMANDS) WITH FREESURFER with "Subject29masked2.mgz" and "Subject29_mri_freesurfer2.mgz"<br>AND HERE IN THE SOURCE MODEL IS WHERE I GET THE PROBLEM.<br>
<br><br><b style="color:rgb(51,51,255)">%CREATE THE MESH</b><br><div>bnd = ft_read_headshape('29_mri-oct-6-src.fif', 'format', 'mne_source');</div><div>figure;ft_plot_mesh(bnd);</div><div><br><br>
</div>
<div><b style="color:rgb(51,51,255)">%CO-REGISTRATION</b><br></div><div>mri_norm = ft_read_mri('/home/mlizarazu/public/Exchange/Mikel/Subject29/mri/orig-nomask.mgz');</div>
<div>cfg = [];</div><div>cfg.method = 'interactive';</div><div>mri_norm_ctf = ft_volumerealign(cfg, mri_norm);</div><div><br></div><div><br></div><div>mri_norm_ctf = ft_convert_units(mri_norm_ctf, 'cm');</div>
<div>T = mri_norm_ctf.transform*inv(mri_norm_ctf.transformorig);</div><div>bnd = ft_read_headshape('29_mri-oct-6-src.fif', 'format', 'mne_source');</div>
<div>sourcespace = ft_convert_units(bnd, 'cm');</div><div>sourcespace = ft_transform_geometry(T, sourcespace);</div><br><br><b style="color:rgb(51,51,255)">%VOLUME MODEL</b><br>cfg = [];<br>cfg.coordsys = 'spm';<br>
cfg.output = {'brain'};<br>seg = ft_volumesegment(cfg, mri_norm);<br><br>cfg = [];<br>vol = ft_prepare_singleshell(cfg,seg);<br>vol.bnd = ft_transform_geometry(T, vol.bnd);<br><br><b style="color:rgb(51,51,255)">%PLOT</b><br>
figure;hold on;<br>ft_plot_vol(vol, 'facecolor', 'none');alpha 0.5;<br>ft_plot_mesh(sourcespace_ctf, 'edgecolor', 'none'); camlight <br><br><br><br><br>When plotting i have the problem that you see in the photos... Hope we can solve this.<br>
<br>Thank you.<br><br><br><br>Best whises<br><br><br>Ion<br><br><br><br><br><br><br><br><div class="gmail_quote">2012/1/26 Stolk, A. <span dir="ltr"><<a href="mailto:a.stolk@fcdonders.ru.nl" target="_blank">a.stolk@fcdonders.ru.nl</a>></span><div>
<div class="h5"><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div style="font-size:12pt;font-family:Times New Roman"><p>Hi Ion,</p>
<p> </p>
<p>Could you specify some more details so we can reproduce your bug. Preferably by including a small test script with the same operations applied to the testdata (as in the tutorial).</p>
<p> </p>
<p>Best regards,</p>
<p>Arjen</p>
<p></p><div><br>----- "Ion Lavado" <<a href="mailto:lavado@gmail.com" target="_blank">lavado@gmail.com</a>> schreef: <br>> Van: "Ion Lavado" <<a href="mailto:lavado@gmail.com" target="_blank">lavado@gmail.com</a>><br>
</div>> Aan: "Email discussion list for the FieldTrip project" <<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a>><br>> Verzonden: Donderdag 26 januari 2012 13:39:41<br>
> Onderwerp: Re: [FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace<div><div><br>><br>> Thank you for your help. I realigned it to Tailarach prior to freesurfer processing. Any idea?</div>
</div><p></p><div><div>
<div><br>> </div>
<div>Ion <br>>
<div class="gmail_quote">> 2012/1/19 Stolk, A. <span dir="ltr"><<a href="mailto:a.stolk@fcdonders.ru.nl" target="_blank">a.stolk@fcdonders.ru.nl</a>></span><br>>
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote">
<div>
<div style="FONT-FAMILY:Times New Roman;FONT-SIZE:12pt">>
<p>Hi Ion,</p>
<p> </p>
<p>Did you realign your anatomical image to Talairach space (and not accidentally to MNI space) prior to the processing with Freesurfer?</p>
<p> </p>
<p><a href="http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures" target="_blank">http://imaging.mrc-cbu.cam.ac.uk/imaging/FindingCommissures</a></p>
<p> </p>
<p>Best regards,</p>
<p>Arjen</p>
<p> </p>
<p><br>> ----- "Ion Lavado" <<a href="mailto:lavado@gmail.com" target="_blank">lavado@gmail.com</a>> schreef: <br>> > Van: "Ion Lavado" <<a href="mailto:lavado@gmail.com" target="_blank">lavado@gmail.com</a>><br>
> > Aan: <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>> > Verzonden: Donderdag 19 januari 2012 09:25:16<br>> > Onderwerp: [FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace</p>
<div>> <br>> ><br>> > Hello, i'm trying a source reconstruction of event related fields using minimun-norm estimates and i get a problem with vol and sourcespace. When plot them together the vol doesn't fit the sourcespace. I adjunted in the mail two images where you can see what i get. It looks like that there isn't any problem of coordinate system also the units seem to be ok. I also procesed all the file with freesurfer so i suppose there is no problem with the orig-nomask.mgz.</div>
<p></p>
<div>>
<div>Hope anyone can help me. Thank you very much.</div>
<div><br>> > </div>
<div>Ion</div><br>> </div>> _______________________________________________<br>> > fieldtrip mailing list<br>> > <a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>> > <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div>
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