<html><head><style type='text/css'>p { margin: 0; }</style></head><body><div style='font-family: Times New Roman; font-size: 12pt; color: #000000'><P>Hi Ion,</P>
<P> </P>
<P>Thanks for providing the details. I cannot test run these commands myself as they point to your private dataset and not the example 'Subject01'. However, scanning through the text, it seems to me you have used the correct lines of code. Perhaps something may have gone wrong with the interactive volumealignment procedures, 3 times in total. Did you manually press the l, r, and n buttons when selecting the left and right ear, and nasion in the first and third interactive alignment steps? And, in contrast, did you press the a, p, and z buttons when selecting the anterior and posterior commisures and an interhemispheric point (see link in previous mail) in the second alignment step? This is the 'realign to talairach' part of the code.</P>
<P> </P>
<P>Best regards,</P>
<P>Arjen</P>
<P> </P>
<P> </P>
<P> </P>
<P> </P>
<P> </P>
<P><BR>----- "Ion Lavado" <lavado@gmail.com> schreef: <BR>> Van: "Ion Lavado" <lavado@gmail.com><BR>> Aan: "Email discussion list for the FieldTrip project" <fieldtrip@donders.ru.nl><BR>> Verzonden: Vrijdag 27 januari 2012 09:33:10<BR>> Onderwerp: Re: [FieldTrip] Source reconstruction with MNE problem: vol doen's fit sourcespace<BR>><BR>> Ok, thank you for your time Arjen. This is what i've done:<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>> <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>> <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>> <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>> 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>> cfg.filename = 'Subject29masked2';<BR>> ft_volumewrite(cfg, seg);<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>> <B style="COLOR: rgb(51,51,255)">%CREATE THE MESH</B><BR>> </P>
<DIV>bnd = ft_read_headshape('29_mri-oct-6-src.fif', 'format', 'mne_source');</DIV>
<DIV>figure;ft_plot_mesh(bnd);</DIV>
<DIV><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>> <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>> cfg = [];<BR>> vol = ft_prepare_singleshell(cfg,seg);<BR>> vol.bnd = ft_transform_geometry(T, vol.bnd);<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>> When plotting i have the problem that you see in the photos... Hope we can solve this.<BR>> <BR>> Thank you.<BR>> Best whises<BR>> Ion<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><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>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 class=im>> <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 class=h5>> <BR>> ><BR>> > Thank you for your help. I realigned it to Tailarach prior to freesurfer processing. Any idea?</DIV></DIV>
<P></P>
<DIV>
<DIV class=h5>>
<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></DIV><BR>> > _______________________________________________<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><BR>> > </BLOCKQUOTE></DIV><BR>> > </DIV><BR>> > _______________________________________________<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></DIV></DIV></DIV><BR>> _______________________________________________<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><BR>> </BLOCKQUOTE></DIV><BR>> <BR>> _______________________________________________<BR>> fieldtrip mailing list<BR>> fieldtrip@donders.ru.nl<BR>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</div></body></html>