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</o:shapelayout></xml><![endif]--></head><body lang=NL link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Jan-Mathijs,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks, this indeed did the trick!<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Ergo, forward warping of coordinates ‘pos’ work like this:<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>mri_realign_mni=ft_volumenormalise([],mri_realign)<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>mnipos=ft_warp_apply(mri_realign_mni.params,ft_warp_apply(mri_realign_mni.initial, pos,'individual2sn')<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Inverse warping returns coordinates of mnipos in subject space (ctfpos):<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>posback=ft_warp_apply(mri_realign_mni.params,mnipos,'sn2individual')<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><span style='mso-list:Ignore'>-<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>ctfpos=</span><span lang=EN-US> </span><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>ft_warp_apply(pinv(mri_realign_mni.initial),posback)<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Stan<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl] <b>On Behalf Of </b>jan-mathijs schoffelen<br><b>Sent:</b> dinsdag 23 september 2014 7:22<br><b>To:</b> FieldTrip discussion list<br><b>Subject:</b> Re: [FieldTrip] leadfields MNI-coordinates<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Hi Stan,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Part of the solution you’re looking for probably lies in the fact that both the forward and inverse warp are non-linear transformations (when the volumetric normalization is done with cfg.nonlinear = ‘yes’). In other words, the inverse warp cannot be achieved by a simple linear transformation (i.e. the (p)inv of a xxx.transform matrix). Fortunately, ft_warp_apply supports both ft_warp_apply(params, pos, ‘individual2sn’), and ft_warp_apply(params, pos, ‘sn2individual’). The latter aims to achieve the inverse warp you’re looking for. Probably you need to then also still apply the inverse of mri_realign_mni.initial.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Best,<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><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Sep 22, 2014, at 5:12 PM, Stan van Pelt <<a href="mailto:s.vanpelt@psych.ru.nl">s.vanpelt@psych.ru.nl</a>> wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><p class=MsoNormal>Hi Eelke,<br><br>Thanks a lot, I seem to have missed that thread, very informative!<br>However, I seem not able yet to do the inverse warping, from MNI-coordinates <br>to CTF-coordinates.<br><br>- First I do<br>mri_realign_mni=ft_volumenormalise([],mri_realign)<br><br>- This gives me the transformation/normalization parameters from ctf->mni<br>- As an example, I apply them to a random coordinate, here [3 5 6]:<br>mnipos=ft_warp_apply(mri_realign_mni.params,ft_warp_apply(mri_realign_mni.initial,[3 <br>5 6]),'individual2sn')<br><br>- This gives me mni-coordinates -6.0652 -21.7174 -57.2273<br>- But how can I do the reverse?<br>- If I do<br>round(ft_warp_apply(pinv(mri_realign_mni.transform),mnipos))<br> I don't get [3 5 6]<br><br>- It seems to me I should do something like<br>ctfpos=ft_warp_apply(pinv(mri_realign_mni.params, <br>mnipos),mnipos,'individual2sn')<br> or so, but I am not getting it right...<br><br>Best,<br>Stan<br><br><br>-----Original Message-----<br>From: <a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> <br>[<a href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>] On Behalf Of Eelke Spaak<br>Sent: maandag 22 september 2014 13:20<br>To: FieldTrip discussion list<br>Subject: Re: [FieldTrip] leadfields MNI-coordinates<br><br>Hi Stan,<br><br>Have a look at this recent thread on the list (4 messages, Tom and me, this <br>is the starting message):<br><a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2014-August/008362.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2014-August/008362.html</a><br>I think that might help you.<br><br>Groetjes,<br>Eelke<br><br>On 22 September 2014 12:44, Stan van Pelt <<a href="mailto:s.vanpelt@psych.ru.nl">s.vanpelt@psych.ru.nl</a>> wrote:<br><br><o:p></o:p></p><p class=MsoNormal>Dear FieldTrippers,<br><br><br><br>For sourceconstruction (CTF275 MEG data) at specific ROIs, I want to<br>compute leadfields at specific (MNI-)coordinates in the brain. I am<br>trying to find out how that is most easily done using FieldTrip<br><br><br><br>- The most intuitive way seems to me to warp the MNI template to the<br>individual’s brain<br>(<a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_</a><br>individual_head_space_that_are_all_aligned_in_mni_space)<br>, and then apply the warping parameters to the ROI’s MNI-coordinates,<br>and enter the subsequent CTF-coordinates into ft_prepare_leadfield.<br>However, I am not sure where exactly I can find these parameters, and<br>how to apply them. Are these the ones in [gridsrc].params (output <br>ft_sourcemodel)?<br><br>- Alternatively, should I run ft_volumenormalise to warp the brain to<br>MNI-space, and then inversely apply the warping parameters to the<br>ROI’s MNI-coordinates? Again, where can I find the warping parameters<br>in this case, and how should they be applied?<br><br><br><br>Best,<br><br>Stan<br><br><br><br>-<br>Stan van Pelt, PhD<br>Donders Institute for Brain, Cognition and Behaviour Centre for<br>Cognition Montessorilaan 3, B.01.34<br>6525 HR Nijmegen, the Netherlands<br>tel: +31 24 3616288<br><br><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></p><p class=MsoNormal><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br><a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></p></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-family:"Helvetica","sans-serif";color:black'>Jan-Mathijs Schoffelen, MD PhD <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Max Planck Institute for Psycholinguistics,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Nijmegen, The Netherlands<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a><o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'>Telephone: +31-24-3614793<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Helvetica","sans-serif";color:black'><a href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a><o:p></o:p></span></p></div></div></div></div></div></div></div></div></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>